Study your flashcards anywhere!

Download the official Cram app for free >

  • Shuffle
    Toggle On
    Toggle Off
  • Alphabetize
    Toggle On
    Toggle Off
  • Front First
    Toggle On
    Toggle Off
  • Both Sides
    Toggle On
    Toggle Off
  • Read
    Toggle On
    Toggle Off

How to study your flashcards.

Right/Left arrow keys: Navigate between flashcards.right arrow keyleft arrow key

Up/Down arrow keys: Flip the card between the front and back.down keyup key

H key: Show hint (3rd side).h key

A key: Read text to speech.a key


Play button


Play button




Click to flip

81 Cards in this Set

  • Front
  • Back
What do plants RARELY derive energy from?
They typically do not break down amino acids.
Do animals derive energy from AAs?
Yes, they may do so, especially carnivores. We get about 4kcal/g. However, it is important to remember that proteins are not the first source of energy. It only occurs if we need it or if we consumed too much protein.
In amino acid catabolism in mammals what are amino acids intially broken down to?
Amino acids from dietary proteins and intracellular proteins are first broken down into NH4 and Carbon Skeletons. The ammonia goes into to urea cycle. The carbon skeletons go into the CAC where we get energy from.
Where does amino acid catabolism typically occur?
It mostly occurs in the liver.
Where does most amino acid metabolism occur?
It mostly occurs in the liver.
Where does the initial breakdown of proteins take place?
The initial breakdown is in the stomach and then in the intestines.
What is the pH of the gastric juice in the stomach? What is it able to do?
The pH is about 1.0-2.5. It kills bacteria and unfolds proteins (some fibrous, some globerular).
What is pepsin and how is it involved in the catabolism of proteins.?
Pepsin is an enzyme in the stomach that cleaves large proteins into oligopeptides (small peptides).
After pepsin in the stomach converts proteins to oligopeptides where do the oligopeptides go to next?
They go to the small intestine (pancreas).
How are the pancreas and small intestine involved in the catabolism of proteins?
The pancreas makes and excretes zymogens (inactive enzymes). The zymogens are activated in the intestine (into trypsin and chymotrypsin). These are specific to AAs in oligopeptides into and breaks them down to smaller oligopeptides.
After oligopeptides have been converted to smaller oligopeptides in the small intestine what happens to them?
They are digested into AAs by carboxypeptidases and aminopeptidases.
How do carboxypeptidases digest oligopeptides?
They digest them from the carboxyl group end.
How do aminopeptidases digest oligopeptides?
They digest them from the amino end.
Inactive zymogens become what?
They become active proteases.
Name an inactive zymogen in the stomach. Where does it become activated? What is the active protease named?
The inactive zymogen in the stomach is PEPSINOGEN (which is secreted by the gastric glands). The pepsinogen is activated to PEPSIN in the STOMACH. (inactive and active forms in stomach)
Name 3 inactive zymogens secreted by the pancreas?
1. Trypsinogen

2. Chymotrypsinogen

3. Procarboxypeptidases
Name the 3 inactive zymogens in the pancreas and show what they are activated to? Where are they activated?
They are all activated in the small intestine.

1. Inactive Trypsinogen becomes active TRYPSIN

2. Inactive chymotrypsinogen becomes active CHYMOTRYPSIN

3. Inactive procarboxypeptidases becomes active CARBOXYPEPTIDASE
If secreted zymogens are blocked from entering the small intestine what can occur?
Acute Pancreatitis. They are activated prematurely in the pancreas and they begin to attack pancreatic tissue. This is painful, harmful, and sometimes fatal. It needs to be caught quickly or the enzymes essentially digest the pancreas.
How are most globular proteins digested?
As discussed on earlier notecards : The proteins are unfolded in the stomach by gastric juices and cleaved by pepsin to become oligopeptides. These oligopeptides are then further digested into smaller oligopeptides in the small intestine by trypsin and chymotrypsin. They are then digested by carboxypeptidases and aminopeptidases into amino acids.
How are some fibrous proteins digested?
SOME are only partially digested. This occurs because they are wound around eachother and are thus protected from digestion and excreted.
Some plant proteins are protected from digestion by what?
Protected by CELLULOSE HUSKS. So, like fibrous proteins, some are only partially digested.
What is the general path that amino acids take from the intestine to the liver?
What is the first reaction in the AA digestion process in the liver?
What is an essential co-factor for transamination in the liver?
PLP (pyridoxal phosphate) is essential. It is required for all aminotransferases.
What is an aminotransferase?
An enzyme that catalyzes a type of reaction between an amino acid and an α-keto acid. Specifically, this reaction (transamination) involves removing the amino group from the amino acid, , leaving behind an α-keto acid.
Where does PLP come from?
It is a coenzyme form of vitamin B6.
What is a common intermediate involved in the transamination rxn in the liver?
What is a by-product of the transamination rxn in the liver?
alpha-keto acid
What is the second rxn in the AA digestion process?
Glutamate oxidative deamination in hepatocytes.
What is one of the reactants in Glutamate oxidative deamination in hepatocytes?
Glutamate, which is a common intermediate from the transamination rxn in the liver.
What is the purpose of the glutamate oxidative deamination rxn in hepatocytes?
It is a regulated process that prepares ammonia for entry into the urea cycle.
What are the two products of glutamate oxidative deamination?
Alpha-ketoglutarate and ammonia (NH4+).
Alpha-ketoglutarate is one of the products of glutamate oxidative deamination. What can it go on to be a part of?
It can go on to transamination, the CAC, or gluconeogenesis.
Ammonia is a product of glutamate oxidative deamination. What can it go on to become a part of?
The urea cycle.
Is glutamate oxidative deamination in hepatocytes the only way to 'handle' ammonia?
No, there are two other ways if it comes from tissues other than the liver.
What happens when NH3/NH4+ is formed in extrahepatic tissue?
It is formed there but it must be transported to the liver to be metabolized. However, it is toxic so glutamine transports it to the liver in the form of an amino group (NH2+).
How are kidneys involved in the response to acidosis?
There are two possibilities. They can get rid of glutamine/NH4+ or create a buffer in the pH.
Ordinarily what processes glutamine? What occurs during acidosis?
Ordinarily, the liver processes most of the glutamine, but during acidosis the kidneys extract a greater fraction of the blood glutamine. In the kidneys, NH4+ IS RELEASED FROM THE GLUTAMINE and then combines with metabolic bases to form salts which can be excreted into the urine.
How is bicarbonate involved in acidosis?
It can be formed when the kidneys respond to acidosis. It is formed by the decarboxylation of alpha-ketoglutarate. It BUFFERS the blood, raising the pH.
What is the glucose alanine cycle?
It is another way to transport amino groups non-toxically (using alanine as a carrier).
How do most AQUATIC species excrete N-compounds?
They excrete nitrogen as ammonia (the dilution solution).
How do BIRDS AND REPTILES excrete N-compounds?
They excrete amino nitrogen as URIC ACID ('the windshield solution').
Besides aquatic species, birds, and reptiles how do most other terrestrial animals excrete N-compounds?
Other terrestrial animals (incl. humans) excrete UREA (the detox solution).
Describe the general sequence from amino acid to urea?
1. Transfer nitrogen from any AA to GLUTAMATE.

2. TRANSPORT glutamate from the CYTOSOL into the MITOCHONDRIA

3. Transfer the nitrogen from glutamate to CARBAMOYL PHOSPHATE (C.P.)(it carries th amino group from the AA).

4. Transfer the nitrogen from c.p. to ORNITHINE to form CITRULLINE.

5. TRANSPORT citrulline out of the mitochondria.

6. Urea Cycle : Citrulline to ORNITHINE.
What energy is required in forming carbamoyl phosphate (c.p.) from AA?
It requires two ATPs to form c.p.
The urea cycle and the kreb's cycle are connected ('the kreb's bicycle') by a number of shared intermediates especially ? and ?.
They are esp. linked by FUMARATE AND ASPARTATE.
In the Urea cycle AAs are the source for NH4+ which is put in to the cycle. What do we get OUT from this?
AAs are the source for NH4+, when NH4+ is put in we get UREA out.
In the urea cycle AAs are the source for aspartate. When aspartate is put in what do we get OUT?
What are the 3 different sources of energy in the urea cycle?
1. CP synthesis

2. Citrulline to arginine succinate

3. CAC
What does CP synthesis put in to the Urea cycle? What do we get out of this?
It puts IN 2 ATP. We get OUT 2 ADP. This results in -2 ATP energy equivalents (bc we put 2 in).
What does the formation of citrulline to arginine succinate put in to the urea cycle? What do we get out?
It puts IN 1 ATP. We get out 2 Pi. This results in -2 ATP equivalents.
What does the CAC put into the urea cycle? What do we get out?
It puts in NAD+. We get out NADH. This results in +2.5 ATP equivalents.
What is the NET energy output from the urea cycle? Explain.
-1.5 ATP equivalents. Because you put in 4 and get out 2.5. See slide #22 in class notes.
How is arginine involved in the regulation of AA catabolism?
Arginine (or any AA) is a key regulatory molecule. An increased concentration of it accelerates the rate of making carbamoyl phosphate.
In the long term AA catabolism needs regulation of ? ?. In the short term it involves ? regulation.
In the long term there is regulation of enzyme synthesis. In the short term it is allosteric regulation.
Genetic defects in urea cycle enzymes may reduce one's ability to do what?
May reduce the ability to digest protein rich foods. This can cause AAs and toxic NH3 to accumulate.
What is the solution to genetic defects in urea cycle enzymes?
Restrict AA (protein) intake. So you have a low protein diet, but you can not completely eliminate it because it is essential.
Amino acid degradation involves the degradation of what?
Involves the degradation of the carbon skeleton of AAs.
Amino acid degradation is an example of what?
It is an example of converging catabolic pathways. 20 AAs converge to 5 intermediates of the CAC.
What are the 5 intermediates of the 20 converging AAs?
1. Alpha-ketoglutarate

2. Succinyl-CoA

3. Fumarate

4. Oxaloacetate

5. Acetyl-CoA

(Sometimes pyruvate is counted as a sixth)
What is a glucogenic AA?
It is degraded and converted to glucose.
What is a ketogenic AA?
It is degraded and converted to ketone bodies.
Name 4 key cofactors in AA metabolism?
1. PLP

2. biotin

3. tetrahydrofolate

4. S-Adenosylmethionine

2, 3, and 4 are all involved in the transfer of Carbon containing groups. PLP is inv. in transamination rxns.
Nicotinate (niacin) can be converted from what? What is this a precursor for?
It can be converted from tryptophan but it is not very efficient. Niacin is a precursor of NAD and NADP.
What is the most prevalent human genetic disorder affecting AA catabolism?
Phenylketonuria is the most prevalent. It occurs in <8/100,00 births.
What is the defective process in phenylketonuria?
The conversion of phenylalanine to tyrosine.
What is the defective enzyme in phenylketonuria?
Phenyalanine hydroxylase.
What are the possible symptoms and effects of phenylketonuria (PKU)?
Early death, neonatal vomiting, and mental retardation.
How is phenylalanine hydroxylase involved in phenyketonuria?
If it is inactive or present in low concentrations phenyalanine is not processed and accumulates.
PKU results from a defective ? or ?.
A defective enzyme or cofactor.
In PKU what does an accumulation of Phe (phenylalanine) lead to? Who is this esp. important for?
It leads to defective neural tube development and mental retardation. This is esp. important for infants. There is routine screening for this at birth and it can be controlled through the diet.
What happens when the breakdown of Phe is blocked?
PKU. Phe accumulates and a secondary metabolic pathway for Phe is utilized where it is broken down to phenylpyruvate (a phenyl-ketone). This then becomes either phenylacetate or phenyllactate.
What is the old way to detect PKU?
One of the products, phenylacetate, has a characteristic odor in the urine.
In PKU accumulation of Phe and its metabolites may prevent what by competition?
May prevent transport of important AAs from the blood to the brain.
Screening for PKU in newborn babies is ? and ?.
It is easy and very cost effective.
What does treatment of PKU involve?
It involves the restriction of Phe intake in the diet. Anyone with PKU must avoid aspartame, which is a dipeptide of Asp and the Me-ester of Phe (so it contains Phe).
Are defective enzymes the only cause of PKU?
No. It is only the most common form. The situation is more complex it the problem involves the cofactor THB (tetrahydrobiopterin). It requires more than just controlling diet.
What is defective when PKU involves THB?
The enzyme dihydrobiopterin reductase is defective.
If the cause of PKU is THB related does restricting Phe intake help the problem? Explain.
It helps solve part of the problem but it is also necessary to supply precursor of neurotransmitters. This is because THB is also required for the synthesis of the neurotransmitters norepinephrine and serotonin.
What are the only 3 amino acids primarily metabolized outside of the liver?
1. Valine

2. Isoleucine

3. Leucine

(the other 17 are primarily metabolized in the liver)
What is maple syrup urine disease?
It is the result of a defective defective enzyme in the catabolism of branched chain AAs. The defective enzyme is branched-chain alpha keto acid dehydrogenase complex.