Module 11 - Amino Acid Degradation and the Urea Cycle Flashcards
Why do we need to eat protein?
in the normal state, we have no reservoir of amino acids to synthesize proteins, and thus need them in our diet everyday.
How much protein do we need to eat?
The average person requires 70-100 g of dietary protein per day to maintain the amino acid pool
How are proteins digested?
intact proteins are too large to be absorbed in our small intestine, the digestion process breaks down proteins into primarily amino acids, as well as a small amount of di- and tri-peptides
What is proteolysis?
The process whereby peptide bonds within proteins are cleaved
a hydrolytic reaction where a water molecule is added across a peptide bond
proteolysis begins in the stomach and continues on in the small intestine, where protein digestion is completed
What role does the mouth play in protein digestion?
First, it liquefies the protein in the food that increases its surface area and makes it a better substrate for the proteases it will encounter in the stomach in small intestine.
Additionally, chewing and having the protein in your mouth for a certain period of time triggers neural effects that prepare the stomach for the protein that is on its way
What role does the stomach play in protein digestion?
the neural effects that result from chewing food stimulate special cells in the stomach to secrete gastric juice, in amounts up to one litre in volume.
Gastric juice has a very low pH of around 2
The other ingredients in gastric juice include gastrin and pepsin.
Why does the low pH help in protein digestion?
It causes denaturation, or the unfolding, of proteins. This facilitates the degradation of proteins, since unfolding of proteins makes the peptide bonds, many of which are buried in the interior of the folded protein, accessible to proteases.
The low pH also serves as an antiseptic, destroying many bacteria and viruses that are ingested when we eat.
How do gastrin and pepsin help with protein digestion?
Gastrin is a peptide hormone that is secreted by special cells in the stomach. Its primary role is to stimulate acid secretion into the stomach.
Pepsin, is a protease that cleaves the peptide bonds involving hydrophobic amino acids. So while this protease doesn’t completely digest a protein, it does break it up into smaller segments which facilitates the next round of proteolysis that occurs in the small intestine.
How does the small intestine help with protein digestion?
Pancreatic juice contains several additional proteases, each recognizing different types of peptide bonds.
Pepsin cleaves peptide bonds following a hydrophobic amino acid,
Trypsin cleaves bonds following arginine or lysine;
Chymotrypsin cleaves bonds following aromatic amino acids;
Elastase cleaves bonds after amino acids that have smaller, hydrophobic side chains. The carboxypeptidases and aminopeptidases cleave bonds working from either end of peptides with little specificity.
This array of proteases causes proteins to be rapidly degraded into free amino acids.
How are the enzymes themselves protected from being degraded by their own proteolytic activity?
all of the proteolytic enzymes are initially synthesized in an inactive form called a zymogen, and are activated by having a small portion of their polypeptide backbone cut off which allows them to properly fold into active enzymes.
How is the inactive pepsinogen activated to pepsin?
pepsinogen has a 44 amino acid masking sequence on one end of the protein.
When this is cut off, the protein changes conformation and forms a cleft which is the active site where polypeptide regions fit and are cleaved by pepsin
What triggers the removal of the masking sequence in pepsinogen?
When pepsinogen is secreted in the gastric juice, the low pH causes a small degree of conformational change in pepsinogen which allows it to self-cleave the masking sequence, forming a small number of active pepsin molecules.
These active proteases molecules in turn attack other pepsinogen molecules, converting them to active pepsin molecules.
This self-activation process is called autocatalysis.
After digestion of protein is accomplished, continued activity of proteases is not desirable as they will start attacking proteins on the surface of cells. How does the protease stop working?
proteases self-inactivate; they chemically-attack and degrade each other when there is no dietary protein to act on, ensuring that protease activity is terminated when not needed.
What is the First Step in the Degradation of Amino Acids?
Nitrogen Removal
there are two components of amino acids that we need to consider separately since they are handled by distinct mechanisms in the cell.
The two components are the amino group and the carbon skeleton of the amino acids.
the excess amino groups are eventually secreted from our bodies in the form of urea, while the carbon skeletons are converted into α-keto acids, which can be oxidized for energy production or in some cases converted to glucose via gluconeogenesis.
What happens to the amino groups during the catabolism of amino acids?
The amino groups from the amino acids are funneled into one amino acid, glutamate, through a process called Transamination.
The amino group from glutamate is then released as ammonium (NH4+) in a process called Oxidative Deamination.
The combined reactions of Transamination and Oxidative Deamination are collectively referred to as Transdeamination.
The ammonium is then used to synthesize urea, which is excreted from the body.
Urea production occurs only in the liver
Step 1 - Transamination (This occurs in the cytosol)
the transamination reaction, which gathers the amino groups from 17 amino acids (excluded are glutamate, lysine, and threonine; the latter two are catabolized differently) into the amino acid glutamate.
This reaction is catalyzed by aminotransferases, which are specific for the amino group donor.
All 17 of the aminotransferases transfer the amino group from the amino acid substrate to α-ketoglutarate, converting it to glutamate.
The amino acid from which the amino group was removed is converted to a corresponding α-keto acid.
It should also be noted that aminotransferases require pyridoxal phosphate, which is derived from vitamin B6, as a coenzyme.
The nomenclature for aminotransferases are based on the amino acid donor
the enzyme that transfers the amino group from alanine to α-ketoglutarate, producing glutamate and pyruvate as products, is called alanine aminotransferase
Step 2 – Oxidative Deamination of Glutamate in Liver (this occurs in the mitochondria)
Glutamate undergoes oxidative deamination, which releases the amino group as ammonium (NH4+) and
α-ketoglutarate.
By producing free ammonium in the mitochondria, the very place where it will be used to form urea, the ammonium is prevented from accumulating in the body.
Oxidative deamination of glutamate is catalyzed by glutamate dehydrogenase, located in the mitochondria of liver.
As the name suggests, this enzyme catalyzes the removal of the amino group, as well as the oxidation of glutamate in a two-step process.
The electrons removed are captured either as NADH or NADPH.
This makes the enzyme very unusual, since it can use either NAD+ or NADP+ as a substrate.
How is ammonium that is produced in tissues other than liver converted to urea?
In most tissues, free ammonium is incorporated into glutamine by the enzyme glutamine synthetase
While most amino acids cannot get out of cells, glutamine can and it enters the bloodstream and is transported to liver.
In liver, there is an enzyme called glutaminase, a mitochondrial enzyme, which uses water to cleave ammonium off of glutamine.
The ammonium released is used to synthesize urea.
The glutamate in turn can be acted upon by glutamate dehydrogenase, which releases the second amino group
How is ammonium that is produced in muscle tissue converted to urea?
While a small amount of ammonium is incorporated into glutamine in this tissue, most of it gets transported out of muscle in the form of alanine
the excess amino groups in muscle are collected in the form of glutamate.
Glutamate then undergoes a transamination reaction with pyruvate, catalyzed by alanine aminotransferase, which transfers the amino group from glutamate to pyruvate, forming alanine.
Alanine leaves the muscle, goes to the liver through the blood, and in liver the alanine aminotransferase present there transfers the amino group from alanine to
α-ketoglutarate, reforming glutamate.
summary of how amino groups are brought into the liver mitochondria in order to be used to produce urea
What is an obligate activator?
one that is absolutely required for its target enzyme to have activity
The Urea Cycle
the urea cycle consists of reactions that occur in both the mitochondria and the cytosol.
Because the ammonium is released in the mitochondria, this is where things start.
The first and rate-limiting step in urea synthesis is catalyzed by carbamoyl phosphate synthetase I
In this reaction, ammonium is fused to CO2 and requires the cleavage of two ATP, forming carbamoyl phosphate.
This step is where free ammonium is used in urea synthesis.
following a meal where protein is eaten, the influx of amino acids will increase the nitrogen balance which needs to be re-balanced.
The arginine from dietary protein, as well as glutamate, will lead to an increase in N-acetylglutamate, which in turn will stimulate carbamoyl phosphate synthetase I
The important points to remember about the urea cycle are:
it involves reactions in both mitochondria and cytosol
it is connected to the citric acid cycle by fumarate and aspartate
the rate-limiting enzyme is carbamoyl phosphate synthetase I
regulation is through N-acetylglutamate and arginine
energy cost is 3 ATP (4 high energy bonds) per urea molecule formed
overall reaction is:
Aspartate + NH4+ + CO2 + 3 ATP → urea + fumarate + 2 ADP + AMP + 2Pi + PPi
Urea Cycle – Part 1
In part 1 of this cycle, carbamoyl phosphate combines with ornithine to produce citrulline in the mitochondria.
The enzyme that catalyzes this is ornithine transcarbamoylase.
Citrulline then passes out of the mitochondria into the cytosol where the next phase of the urea cycle occurs.
glutamate provides amino groups used in urea synthesis in two ways
First, free ammonium is cleaved from it by glutamate dehydrogenase, which is used to form carbamoyl phosphate.
Second, glutamate transfers its amino group to form aspartate, which is used later in the urea cycle to add the second amino group onto urea.
Urea Cycle – Part 2
In this part of the cycle, urea is produced and ornithine is replenished, which completes the cycle
In the cytosol, citrulline is acted upon by argininosuccinate synthetase.
In a two-part reaction, citrulline reacts with aspartate to form argininosuccinate.
In this reaction, ATP is cleaved to AMP + PPi which drives the reaction forward.
Argininosuccinate is then acted on by argininosuccinase, which cleaves the substrate into fumarate and arginine.
when arginine is acted upon by the hydrolase arginase, urea is produced along with ornithine.
Why are the three cytosolic enzymes (argininosuccinate synthetase, argininosuccinase, and arginase) are clustered together in a complex?
First, it keeps the pathway intermediates trapped in or near the complex, with the products of one reaction quickly passed along to the next enzyme in the pathway.
This keeps the local concentration of intermediates high, thus increasing the reaction rate of the cycle.
Second, keeping the intermediates sequestered in the complex prevents the intermediates from undergoing unrelated, side reactions which would slow the rate of flux through the urea cycle and inhibit the elimination of excess nitrogen from the cell.
There are strong links between the urea cycle and citric acid cycle which are mediated by fumarate and aspartate
fumarate is produced when argininosuccinate is cleaved;
this fumarate can either go directly to the citric acid cycle or be first converted to malate, which can then move to the mitochondria.
aspartate can be formed when glutamate transfers its amino group to oxaloacetate
The aspartate moves to the cytosol, where it is used to form argininosuccinate, and ultimately provides one of the amino groups present in urea.
How do fish dispose of excess nitrogen via urea?
release ammonium directly through the gills into the surrounding water.
They have no need to spend unnecessary ATP to convert ammonium into urea since the large surface area provided by gills allows fast release and disposal of ammonium
What are Ammoniotelic organisms?
Organisms that eliminate excess nitrogen as ammonium
What are Ureotelic organisms?
organisms which secrete urea
How do reptiles and birds secrete urea?
Excreting urea requires a lot of water since it is water-soluble
Birds and reptiles get around this by disposing of excess nitrogen as uric acid, which is a degradation product of purines.
It is relatively insoluble in water, and rather forms a paste
What are the important parts to remember about the Urea Cycle?
it involves reactions in both mitochondria and cytosol
it is connected to the citric acid cycle by fumarate and aspartate
the rate-limiting enzyme is carbamoyl phosphate synthetase I
regulation is through N-acetylglutamate and arginine
energy cost is 3 ATP (4 high energy bonds) per urea molecule formed
overall reaction is:
Aspartate + NH4+ + CO2 + 3 ATP → urea + fumarate + 2 ADP + AMP + 2Pi + PPi
What are the sources of free ammonium?
Transdeamination of amino acids – this involves reactions catalyzed by amino transferases to produce glutamate, which is then acted on glutamate dehydrogenase which releases free ammonium.
Serine and threonine have alternative catabolic pathways, catalyzed by serine and threonine dehydratase, respectively, both of which release free ammonium
The hydrolysis of glutamine by glutaminase in liver releases free ammonium.
Amino groups from other tissues come to the liver in the form of alanine and glutamine; the free ammonium is released from these two amino acids by transdeamination and glutaminase, respectively.
There is also a fair bit of free ammonium produced in the kidney from the breakdown of glutamine and glutamate, by the actions of kidney-specific glutaminase and glutamate dehydrogenase, respectively.
Finally, there are many nitrogen-containing compounds in the body, such as hormones, neutrotransmitters, purines and pyrimidines, that produce free ammonium when they are degraded.
Which mechanisms keep the levels of free ammonium low?
Formation of urea
Formation of glutamate in muscle by glutamate dehydrogenase;
Formation of glutamine in many tissues by glutamine synthetase
What is a glucogenic amino acid?
one that is catabolized to pyruvate or to an intermediate of the citric acid cycle, since these biomolecules can potentially serve as substrates to produce glucose through gluconeogenesis ex. alanine
What are Ketogenic amino acids?
those that are catabolized to acetyl CoA and/or acetoacetate. Neither acetyl CoA nor acetoacetate can lead to the net synthesis of glucose, but rather to the formation of fatty acids, ketone bodies or their precursors
Five amino acids are both glucogenic and ketogenic…..during the catabolism of these amino acids, the products consist of both acetyl CoA or acetoacetate, as well as pyruvate or a citric acid cycle intermediate
tryptophan,
tyrosine,
threonine,
phenylalanine, and
isoleucine
Summary of amino acid catabolism.
What are Porphyrins?
cyclic compounds that bind Fe2+ or Fe3+; the most common
a familiar porphyrin is heme
also include cytochromes and others molecules.
They have conserved structural features: they consist of four nitrogen-containing pyrrole rings that are linked together; and each pyrrole ring has a side-chain that are unique to different porphyrins.
