Barrow: Amino Acid Metabolism Flashcards
What do amino acids and nucleotides contain that carbs and fats don’t?
Where does it come from?
What are diazotrophs?
Nitrogen
Our diet (not from the air)
Nitrogen fixing bacteria
What occurs during the nitrogen cycle?
N2 from air undergoes biological/abiotic fixation, producing ammoinia and ammonium ions; these are converted by nitrifying bacteria in the soil first to nitrite (NO2-) and then to nitrate (NO3-). Denitrifying bacteria then converts it back to N2 (and it is released into the air), whereas plants reduce nitrate back to ammonium (to be incorporated into proteins).
In the nitrogen cycle, is more nitrate reduced to ammonium (and incorporated into plants) or converted into N2 and released back into the air?
Reduced to ammonium
What is the only way than ammonium ions from the nitrogen cycle can be incorporated into biological molecules?
Through the amino acid glutamate
What is the process of turning glutamate into other amino acids/proteins/nucleotides called? And the reverse?
Assimilation & Degradation
Why do we not use nitrogen directly from the air?
What can do it in the absence of other organisms? What does this demonstrate?
How do humans do it?
It is very unreactive (triple bond between 2 nitrogen atoms)
If oxygen and lightning are present, it can create NO or NO2 (demonstrates how much energy is needed)
Haber-Bosch Process: react with H2 at 400-450 degrees centigrade at 200atm with iron catalyst
What are the names of some of the nitrogen fixing bacteria?
Cyanobacteria (Lake Atitlan - big green swirls), rhizobium bacteria (in root nodules on legumes)
What is the name of the enzyme required to undertake nitrogen fixation? What else does it need?
Nitrogenase (a lot of energy: N2 + 8H+ + 8e- + 16ATP -> 2NH3 + H2 + 16ADP + 16Pi)
Nitrogenase (nitrogen fixing enzyme) is inactivated by what? What ways is this dealt with by the bacteria?
How do some plants assist? What is the visual clue to this symbiotic assistance?
Oxygen - can live anaerobically (forming heterocysts whose cell wall prevents oxygen entry, or decoupling mitochondria and burning off oxygen)
Leguminous plamnts produce leghemoglobin (binds to oxygen and keeps concentration low enough for bacterial nitrogenase to function) = inside of nodules often bright red
Nitrogen has been fixed and converted to ammonium ions. Which biomolecule is then needed to create glutamate? What else is needed?
Alpha-ketoglutarate (citric acid cycle intermediate) - also requires NADPH and ATP
Which is the only amino acid that can obtain nitrogen directly from (and give its nitrogen directly away to) NH4+?
Glutamate
Which four amino acids are found in much higher concentration in cells compared to other aminos?
Alanine, glutamine, glutamate, and aspartate
Major role of glutamate and aspartate = __________ _________________. Glutamate is also important in _____ (__________ _________)
excitatory neurotransmitters, taste, monosodium glutamate
How do organisms conserve their nitrogen stores?
How would it be excreted (if you wanted to)?
Transamination (transfer of amino groups between amino acid to [usually] a keto-acid, producing a new amino acid and a new ketoacid)
Amino group would be transferred to alpha-ketoglutarate (becoming glutamate), and then this would combine with another amino group to create urea (which would be excreted)
General principle of transamination?
Are they reversible?
One of the 2 substrate pairs is often what?
Amino acid 1 + keto acid 2 -> keto acid 1 + amino acid 2
Usually
Glutamate
Transamination of glutamate and pyruvate…
Which is the alpha-keto acid?
What are the products?
How does this tie into energy creation?
Pyruvate
Alpha-Ketoglutarate + alanine
Can be reversed: alanine can be converted to pyruvate, which can then enter the citric acid cycle…
What is the name of the enzyme involved in transamination?
What cofactor do they rely on? Made from? What does it do during the reaction?
What typically accepts amino groups?
What acts as a temporary storage of nitrogen? When does it give it up?
Transaminases
Pyridoxal phosphate cofactor (vitamin B3 [essential - needed in diet] - transfers amino group during the reaction)
Alpha-ketoglutarate
L-Glutamine (when needed for amino acid biosynthesis)
What does the presence in plasma of aminotransferases in plasma indicate? Why?
Where is a lot of amino acid metabolism happening? Which enzymes from this area are useful for tracking disease?
Cell damage (because they are intracellular - they shouldn’t be in your blood)
Liver - aspartate aminotransferases (AST: aspartate to oxaloacetate) and alanine aminotransferase (ALT: alanine to pyruvate)
% of energy needs of carnivores met by amino acids?
What about herbivores? Microorganisms?
90%
Tiny fraction (and microorganisms - varies depending on environment)
When would amino acids in your body undergo oxidative catabolism? [3]
Leftover amino acids (from normal protein turnover)
Dietary amino acids that exceed protein synthesis needs
When carbs/fats are in short supply (starvation, diabetes, etc)
Which enzymes hydrolyse dietary proteins and where do they do it? [1/2+2]
How can these enzymes be useful in the lab?
Pepsin (+ stomach acid) cuts proteins to peptides in stomach
Trypsin and chymotrypsin cut proteins/peptides into smaller peptides in small intestine
Aminopeptidase and caboxypeptidases (A and B) degrade peptides into amino acids in small intestine
[Useful in lab because they chop at specific cleavage points, which can be utilized identify proteins]
What is the name of the precursor molecule type which spawn proteases and peptidases? Why have precursors?
What is the pepsin precursor called?
Zymogens (you have these so that they don’t start just degrading proteins willy nilly)
Pepsinogen
What are proteins broken down to in the stomach (acidic environment + enzymes)?
Which membrane bound protein in the intestines degrades remaining oligopeptides still further? There are _______ ____________ for amino acids and di/tripeptides to allow them into the intestinal cells…
… and what gets into the blood stream? And they go to?
Di/Tri peptides + free amino acids
aminopeptidases, specific transporters
Only free amino acids can enter the bloodstream, and then they go to the liver
What tag is added to proteins to target them for destruction? What is usually degraded?
Where do they get sent for degradation? Broken into?
What can happen to the protein elements?
Ubiquitin (used for misfolded proteins, foreign proteins, or unwanted proteins)
Proteasome (-> peptide fragments and ubiquitin)
Left intact for biosynthesis or amino groups can be removed (by urea cycle)and carbon skeletons can be used for glucose/glycogen synthesis, fatty acid synth, or respiration
