CELL Protein Breakdown and Urea Formation

Question 1

Simple growth principle

when do you have growth?

Answer 1

In the body, there is a very simple principle:

• Growth = Synthesis – Breakdown

This equation applies for all aspects of the body, be it individual proteins, single cells, whole tissues or the whole body.

Question 2

Nitrogen Balance (positive and negative)

how do we get protein?
do we have protein stores?
2 types of protein
what happens to excess proteins?

what is postive nitrogen balance?
what is negative nitrogen balance?

Answer 2

We intake proteins through our diet, there are no specific protein stores in our body. Proteins are either structural or functional, excess protein is broken down and excreted.

Therefore, there should be a balance between input and output.

If we are in positive nitrogen balance, this means the amount of protein/AA we retain exceeds the amount that is broken down and excreted. This is a normal process and occurs in things like growth.

The opposite is negative nitrogen balance when input is superseded by breakdown.

Question 3

Fate of amino acids

what happens to dietary protein?
fate of this? examples
what happens to some proteins in our body?

what happens in nitrogen balance? how is this removed by body?

Answer 3

• We ingest dietary protein which is broken down into AA, there are then a number of fates of these AAs.
• They can be used to make new protein e.g. muscle fibres, enzymes (structural or functional).
• At the same time there are also proteins being broken down
• When in nitrogen balance this breakdown matches the synthesis. Out input is about 100g a day and output 100g a day.

The nitrogen is removed in the liver through formation of urea.

Question 4

In a normal, healthy individual

Answer 4

In a normal, healthy individual the relationship should be balanced

so amino acid pool will get input from dietary intake and lose excess to urea and other products. Amino acid pool to body protein + body protein breakdown will be same.

Question 5

physiological reasons why we may be positive nitrogen balance

2 key examples for this and why

Answer 5

There are physiological reasons why we may be positive nitrogen balance, for example growth in small children or when someone is pregnant, they will be taking in and laying down more protein.

N balance can also take place in response to exercise -> tissue hypertrophy as well as a response to anabolic hormones.

This can be seen in the diagram below, where more of the AAs in the AA pool are being converted into body protein and less body protein is being broken down or excreted.

Question 6

Negative nitrogen balance

3 key reasons for this and why

Answer 6

Negative nitrogen balance may be caused due to protein deficiency

Negative nitrogen balance is also associated more with pathophysiology than physiology. For example, wasting diseases, burns and trauma can all cause this.

It could also be in response to catabolic hormones, or a lack of anabolic ones (e.g. in diabetes). Causing someone to lose body protein mass.

Question 7

Metabolism of Amino Acids

how do you deal with aa?
what is the first step before dealing with aa?
what can the carbon skeleton be used for?

Answer 7

Normal body protein metabolism means dealing with amino acids in two parts. Dealing with the carbon skeleton and the nitrogen.

Note that in essence the first step is the breaking down of protein/polypeptide via peptidases into its constituent amino acids.

Carbon Skeleton:
- The carbon skeleton can be used for energy metabolism or biosynthesis.

Question 8

Removal of Nitrogen:

why must nitrogen be removed?
how is this done? what are the 3 steps?

can urea be formed in muscles? why/

Answer 8

Nitrogen is toxic (adverse effect on neuronal cells) so must be removed safely. Individuals who cannot produce urea often die in infancy.

In mammals, the nitrogen is converted to the non-toxic neutral compound urea and excreted in the urine.

The process by which the amino acid nitrogen is transferred to urea is a three-step process:

• Transamination
• Formation of ammonia
• Formation of urea.

Note urea cannot be formed in muscle as the enzyme is not present, the carbon skeleton can be obtained however and used for energy.

Question 9

Transamination

what happens in transamination?
give 3 examples of keto acids - why are these useful? name process

what enzyme does this?
name 2 important ones

Answer 9

In transamination, the nitrogen as part of the α-amino group is transferred to an α-keto-acid to become a new amino acid.

α-ketoglutarate, pyruvate and oxaloacetate are α-keto acids

The enzymes that do this are transaminases, there are quite a lot of different types of transaminases. The most important are the alanine (ALT) and aspartate (AST) transaminases. As explained above, they transfer an amino group from an AA to an α-keto acid.

α-ketoglutarate, pyruvate and oxaloacetate can be oxidised or converted to make glucose (supplementing gluconeogenesis).

Question 10

alanine (ALT) allows

Answer 10

Alanine + α-ketoglutarate -> pyruvate and glutamate

Question 11

aspartate (AST) allows

Answer 11

Aspartate + α-ketoglutarate -> Oxaloacetate (/oxaloacetic acid) and glutamate

Question 12

Glutamate - use?

Answer 12

Glutamate is a way the body can transport potentially toxic Nitrogen.

Question 13

high levels of AST and ALT in the blood

primarily found where?
so if high levels found in blood, indication?

Answer 13

The transaminases are primarily liver enzymes so can be used diagnostically, high levels of AST and ALT in the blood are indicative of liver damage -> normally shouldn’t be found in plasma.

Question 14

So, if we input the alanine and α-ketoglutarate into the diagram above we get

what does this reaction require?

Answer 14

Alanine + α-ketoglutarate -> pyruvate and glutamate

Alanine donates its α-amino group to α-ketoglutarate to give glutamate and pyruvate. This reaction requires vitamin B6

Question 15

Formation of Ammonia

what is used to make ammonia? what enzyme is required? where is this present?

what will this yield?

NAD and NADPH - what is used for degradtion? synthesis?

Answer 15

So, what happens to this glutamate?

Glutamate can release the ammonia by action of a second enzyme, glutamate dehydrogenase that is present in the mitochondrial matrix (transamination occurs in cytosol).

It will yield back α-ketoglutarate.

NAD or NADP can be used, however it is usual for NAD to be used for degradation and NADPH for synthesis.

Question 16

Why is glutamate very useful?

what can it interchange with? what can it donate and accept?

what is transanimation? what will be the opposite of this?
why is this very important?

Answer 16

Glutamate is a very useful molecule because it is freely interchangeable with the α-keto acids as well as the ability to donate and accept ammonium ions.

In this process you have the transamination to glutamate and then the oxidative deamination back to α-ketoglutarate.

The reason it is very important is because it allows conversion of many amino acids from their original state into glutamate, which can be transported.

However, it is not often transported as glutamate and then re-converted back into something the body can use for energy, while re-synthesising the ammonia which can be fed into the urea cycle.

Question 17

Elimination of Free Ammonia

how is glutamate formed? what can it be used for?

what is the equation and enzyme involved?
what is formed? function of this?

where does this reaction take place?

Answer 17

Glutamate formed because of deamination can be used to transport another nitrogen which part of an ammonium ion is++.

Glutamate + NH4+ + ATP -> Glutamine + ADP
Glutamine synthase

Glutamine is like another transport molecule, a way in which the body can transport the potentially toxic N to the liver.

This is a reaction that often takes place in the periphery, glutamine synthase is widely distributed, especially in blood vessels with a lot of protein breakdown including those blood vessels of the liver itself.

Note the reaction goes both ways so we can resynthesise the glutamate from the glutamine.

Question 18

Removal of Nitrogen Summary

4 steps

Answer 18

1. Transfer of amino groups to α-ketogluterate to form glutamate
2. Glutamate can accept more nitrogen forming glutamine
3. Glutamine is the main transporter of nitrogen
4. Glutamine can donate nitrogen for the biosynthesis of amino acids, nucleotides and NAD+

Question 19

The urea cycle

what does it do?
where are enzymes present? where not?
where does it take place in the cell?

what 3 substrates are required?

Answer 19

The means of excreting nitrogen

Enzymes are present in the liver but not muscle

Takes place in the mitochondria and the cytoplasm

Substrates are bicarbonate, aspartate and ammonium ions (released from glutamine or glutamate)

Question 20

urea

what is urea? how many N atoms? from where?

where does the C=O come from?

why is urea more beneficial?

Answer 20

Here is urea, it has two nitrogen atoms. One of them is donated from aspartate, while the other comes from glutamine/glutamate.

The carbon C=O comes from the carbon skeleton, through using CO2 that has been produced from its breakdown.

Hence, the detrimental products of amino acid degradation can be used to combine to form urea, a non-toxic, soluble compound that can be readily excreted.

Question 21

Both the urea cycle and TCA cycle are linked

where does the CO2 come from and what does it react with? what does this form?

what does this molecule react with? what is fromed?
what does this react with? what is formed?
what is this metabolised into? (2)
what is one of these acted upon by? what does this form?

what happens to the other substrate? what is it converted to and transported to? what is it converted into here and use?

what could be the starting point for this reaxtion?

Answer 21

The CO2 comes from the bicarbonate and reacts with the ammonium ion that has come from glutamine/glutamate, formed by transamination of α-ketoglutarate and α-amino acid. They form Carbamoyl phosphate.

1. Carbamoyl phosphate then reacts with Ornithine to produce Citruline.
2. Citruline reacts with Aspartate to form Argino-succinate.
3. Argino-succinate then is metabolised to Arginine and Fumarate.
4. The Arginine is acted upon by the enzyme arginase which is how ultimately urea is formed.

The fumarate -> Malate which is transported back into the mitochondria and converted into oxaloacetate. The process then continues. ( as oxaloacetate can become asparate if react with an amino acid to form a ketoacid)

The starting point could be thought to be Aspartate, formed by the transamination of α-amino acids, when reacting oxaloacetate (another type of keto-acid) with an α-amino acid. And the formation of the Carbamoyl phosphate

Question 22

Muscle

does muscle have enzymes for urea?
How does muscle use branched amino acids? (example)

what other 2 ways does muscles deal with amino acids?

Answer 22

Muscle doesn’t have the enzymes to form urea, so it doesn’t have the urea cycle.
However, muscle does break down amino acids during prolonged exercise or starvation. Branched amino acids are used for this energy (branches e.g. leucine)
There are two routes by which the remaining amino acids are dealt with.

1. Nitrogen is transferred to alanine via glutamate and pyruvate
2. Circulating/Intracellular Glutamate can be made into glutamine (return to liver)

Question 23

Nitrogen is transferred to alanine via glutamate and pyruvate

what is alanine used for?
what happens to branched aa? (2)

what happens to alanine? where does it go? what does it undergo? what does this yield?

what can this be used for and how? (2)

Answer 23

The muscle can export alanine, it is one of the major exports of muscle that is actively being broken down due to exercise or starvation

Branched AA are taken, the carbon skeleton is used for energy production. Then the NH4 can be used to convert to pyruvate -> Alanine.

Alanine is then exported into the blood and travels to the liver.

The alanine is then converted to glutamate via transamination (reacting with α-ketogluterate) also producing a pyruvate.

The pyruvate can enter the gluconeogenic pathway to form glucose, the glucose can be transported in the blood back to the muscle where it can be used for energy.

The glutamate will then be used along with the CO2 generated to produce urea.

Question 24

Fate of the Carbon Skeleton

what are the 2 sorts of amino acids? what do they form>

where does this occur?
benefits of this?

Answer 24

There are two sorts of amino acids, the keto-genic amino acids and the gluco-genic amino acids. The keto-genic AAs will form ketone bodies, while the gluco-genic AAs can be used by the liver to produce glucose.

Some AAs are in both categories.

Amino acids can feed into different parts of this main carbohydrate pathway.

This occurs in the liver, where most of the gluconeogenic pathway takes place. Amino acids broken down can be converted into intermediates of the TCA cycle. This is good because we can convert this back to glucose.

Question 25

Summary

Answer 25

• Proteins/AAs are not stored
• Excess proteins/AAs are broken down to ammonia and a carbon skeleton
• Ammonia is toxic so has to be removed
• Removal requires transamination and the urea cycle
• Carbon skeletons can be used for the production of glucose, ketone bodies and/or energy

Question 26

PROTEIN and AMINO ACID METABOLISM AFTER A MEAL

what hormone will be high? low?

what will happen in normal individual?

Answer 26

NORMAL METABOLISM (high insulin, low glucagon)

In a normal individual most amino acids from a protein meal will be used for protein synthesis in peripheral tissues such as skeletal muscle.

Excess amino acids can also be used as sources of energy, and the nitrogen derived from their oxidation will be incorporated into urea in the liver and excreted.

Question 27

PROTEIN and AMINO ACID METABOLISM DURING STARVATION

hormones?
what happens during short term starvation?
long term starvation?

Answer 27

In a normal individual: insulin is low, glucagon is high

During short-term starvation there will be a net flow of amino acids from muscle to the liver, with increased production of glucose and urea.

During long-term starvation, tissue protein is “spared” because ketone bodies replace glucose as a major energy fuel for the brain.

Question 28

PROTEIN and AMINO ACID
METABOLISM IN UNTREATED DIABETES

how is this similar to short term starving?

how can this be mediated?

what other conditions see negative nitrogen balance? (4)

Answer 28

Here the negative nitrogen balance associated with short term starvation persists even though the subject is fed, leading to muscle wasting.

Negative nitrogen balance due to decreased protein synthesis and/or increased protein breakdown is also seen in conditions of chronic infections, late stage cancer or trauma, including that following surgery or burns injury.

Some of these effects are mediated by cytokines.