Barrow: Amino Acid Metabolism

Question 1

What do amino acids and nucleotides contain that carbs and fats don’t?

Where does it come from?

What are diazotrophs?

Answer 1

Nitrogen

Our diet (not from the air)

Nitrogen fixing bacteria

Question 2

What occurs during the nitrogen cycle?

Answer 2

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).

Question 3

In the nitrogen cycle, is more nitrate reduced to ammonium (and incorporated into plants) or converted into N₂ and released back into the air?

Answer 3

Reduced to ammonium

Question 4

What is the only way than ammonium ions from the nitrogen cycle can be incorporated into biological molecules?

Answer 4

Through the amino acid glutamate

Question 5

What is the process of turning glutamate into other amino acids/proteins/nucleotides called? And the reverse?

Answer 5

Assimilation & Degradation

Question 6

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?

Answer 6

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

Question 7

What are the names of some of the nitrogen fixing bacteria?

Answer 7

Cyanobacteria (Lake Atitlan - big green swirls), rhizobium bacteria (in root nodules on legumes)

Question 8

What is the name of the enzyme required to undertake nitrogen fixation? What else does it need?

Answer 8

Nitrogenase (a lot of energy: N₂ + 8H⁺ + 8e^- + 16ATP -> 2NH₃ + H₂ + 16ADP + 16P_i)

Question 9

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?

Answer 9

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

Question 10

Nitrogen has been fixed and converted to ammonium ions. Which biomolecule is then needed to create glutamate? What else is needed?

Answer 10

Alpha-ketoglutarate (citric acid cycle intermediate) - also requires NADPH and ATP

Question 11

Which is the only amino acid that can obtain nitrogen directly from (and give its nitrogen directly away to) NH4⁺?

Answer 11

Glutamate

Question 12

Which four amino acids are found in much higher concentration in cells compared to other aminos?

Answer 12

Alanine, glutamine, glutamate, and aspartate

Question 13

Major role of glutamate and aspartate = __________ _________________. Glutamate is also important in _____ (__________ _________)

Answer 13

excitatory neurotransmitters, taste, monosodium glutamate

Question 14

How do organisms conserve their nitrogen stores?

How would it be excreted (if you wanted to)?

Answer 14

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)

Question 15

General principle of transamination?

Are they reversible?

One of the 2 substrate pairs is often what?

Answer 15

Amino acid 1 + keto acid 2 -> keto acid 1 + amino acid 2

Usually

Glutamate

Question 16

Transamination of glutamate and pyruvate…

Which is the alpha-keto acid?

What are the products?

How does this tie into energy creation?

Answer 16

Pyruvate

Alpha-Ketoglutarate + alanine

Can be reversed: alanine can be converted to pyruvate, which can then enter the citric acid cycle…

Question 17

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?

Answer 17

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)

Question 18

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?

Answer 18

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)

Question 19

% of energy needs of carnivores met by amino acids?

What about herbivores? Microorganisms?

Answer 19

90%

Tiny fraction (and microorganisms - varies depending on environment)

Question 20

When would amino acids in your body undergo oxidative catabolism? [3]

Answer 20

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)

Question 21

Which enzymes hydrolyse dietary proteins and where do they do it? [1/2+2]

How can these enzymes be useful in the lab?

Answer 21

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]

Question 22

What is the name of the precursor molecule type which spawn proteases and peptidases? Why have precursors?

What is the pepsin precursor called?

Answer 22

Zymogens (you have these so that they don’t start just degrading proteins willy nilly)

Pepsinogen

Question 23

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?

Answer 23

Di/Tri peptides + free amino acids

aminopeptidases, specific transporters

Only free amino acids can enter the bloodstream, and then they go to the liver

Question 24

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?

Answer 24

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

Question 25

What are the sources of the nitrogen that are removed from our body (in the liver)? [3]

What does it have to be converted into before it can be excreted?

What form does it get excreted in? [3]

Answer 25

Amino acids from ingested proteins, alanine from muscle, glutamine from muscle/other tissues

Glutamate

NH4+, urea, uric acid

Question 26

In what form do plants remove nitrogen?

What about aquatic vertebrates?

Terrestrial vertebrates and sharks?

Birds and reptiles?

Humans and great apes?

Answer 26

Plants conserve all of it

As ammonia (epithelial pass. diffusion, active transport via gills)

Urea (NB: less toxic than ammonia, high solubility)

Uric acid (insoluble, excretion as paste conserves water)

Urea and uric acid

Question 27

What illness can uric acid crystals cause?

Answer 27

Gout

Question 28

How is ammonia/nitrogen transported in the bloodstream?

Where is excess glutamine processed?

What liver enzyme removes ammonia from blood transporter (for excretion)?

Answer 28

As glutamine (or alanine)

Intestines, kidneys, and liver

Glutaminase

Question 29

Glycolysis yields pyruvate. In exercising muscles, this can build up. To avoid conversion to lactate (and build up of lactic acid), what can it be converted to instead?

What is this cycle called? How does it work?

Answer 29

Alanine

Glucose Alanine cycle

Question 30

Why is glutamate converted to glutamine or alanine for transport through the blood?

Answer 30

Glutamate is negatively charged, and alanine/glutamine is neutral. Charged compounds can’t pass through membranes very easily, so it is converted to an uncharged molecule.

Question 31

Where is excess glutamate metabolized?

What is the first step of nitrogen excretion?

Answer 31

In the mitochondria of the liver

Aminos/alanine/glutamine enter liver, are converted to glutamate (just before/after entering mitochondrial matrix). Ammonia is removed (by glutamate dehydrogenase) and added either to oxaloacetate (to form amino aspartate) or used to create carbamoyl phosphate (which is incorporated into orthinine to make citrulline). These two nitrogen-carrying molecules (aspartate/citrulline) then enter the next stage…

Question 32

What is the first nitrogen acquiring reaction as part of nitrogen removal?

What is the second?

Answer 32

Creation of carbamoyl phosphate (by carbamoyl phosphate synthetase I)

Entry of aspartate into urea cycle

Question 33

Through how many intermediate compounds can amino acids enter metabolic pathways? What are they?

Answer 33

6 (Acetyl CoA, pyruvate, alpha-ketoglutarate, succinyl-CoA, fumarate, oxaloacetate)

Question 34

20 coded aminos

How many are non-essential? What does this mean

How many are essential? Which ones [probably not needed]?

What does “conditionally essential” mean?

Answer 34

10 (can be synthesized in body)

9 (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, theonine, tryptophan, valine)

Some needed in higher abundance (in growing animals or during illness)

Question 35

What does it mean for an amino acid to be glucogenic or ketogenic?

Why can’t the product of ketogenic transformation be used in the alternative pathway?

Which aminos are glucogenic AND ketogenic?

Answer 35

Glucogenic (can directly or via pyruvate enter the citric acid cycle, and eventually be converted to glucose), Ketogenic (aminos are converted to Acetyl CoA or Acetoacetyl CoA, and go on to make ketone bodies)

Pyruvate dehydrogenase reaction (pyruvate to Acetyl CoA) is irreversible, and there is no net synthesis of oxaloacetate through the citric acid cycle

Isoleucine, tyrosine, and phenylalanine

Question 36

Total body protein? Just collagen? Turnover daily?

How much protein needs to be eaten daily?

Answer 36

11kg (2.75kg), 250g/day

75g

Question 37

Ketogenic pathway: What does acetyl CoA get converted to?

When are ketone bodies used?

How to tell if someone is using ‘em too much (eg: diabetes)?

Answer 37

Acetoacetate -> acetone and 3-OH butyrate

By brain in absence of glucose

Their breath smells of nail varnish (acetone)

Question 38

What is kwashiorkor?

Hyperammonaemia?

Phenylketonuria?

Alkaptonuria?

Answer 38

Nitrogen in < nitrogen out = low plasma albumin = low osmotic pressure = water stays in tissues (oedema) [extended belly]

Muscle tremors, slurring, coma and death - caused by hereditary defect in urea cycle enzymes (leads to reduced ATP creation)

Can’t break down phe -> tyrosine, buildup of phe and other breakdown metabolites = hyperpigmentation, mental retardation [treatment: avoid phenylalanine]

Black urine, black spots in eyes, caused by defect in tyrosine breakdown enzyme [treatment: restrict tyrosine & phenylalanine]