Term
| Describe the basic structure of an amino acid |
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Definition
| Carbon with an amino group, carboxylic group, H, and R side group |
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Term
| In a polypeptide chain, what is on the left side? What is on the right? |
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Definition
Left: amino-terminal end
Right: carboxyl-terminal end |
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Term
| What are three sources for the amino acid pool? |
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Definition
| Dietary protein, body protein, synthesis (nonessential amino acids only) |
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Term
| Does the body have easy access to amino acids? |
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Definition
| No, amino acids aren't stored like glycogen. They are used right away as protein is ingested. |
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Term
| Define Zero Nitrogen Balance. What kind of organisms have it? |
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Definition
Nitrogen intake = Nitrogen excretion
Mature healthy animals |
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Term
| Define Positive Nitrogen Balance. What kind of organisms have it? |
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Definition
Nitrogen intake > Nitrogen excretion
anabolism>catabolism
Growing animals, pregnancy, recovery from starvation or wasting disease |
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Term
| Define Negative Nitrogen Balance. What kind of organisms have it? |
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Definition
Nitrogen intake < Nitrogen excretion
catabolism>anabolism
Starving, acute injury or infection, senescent animal, or deficiency of an essential amino acid in the diet |
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Term
| Define senescence (adj: senescent) |
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Definition
Aging after maturity, as in an elderly person.
"Or an overripe fruit."- Chris Brown |
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Term
| How do plants and animals form amino acids? |
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Definition
| They incorporate NH4+ into organic molecules.
Many plants and bacteria can synthesize all 20, but humans cannot. |
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Term
| List the essential amino acids |
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Definition
Mnemonic device: PVT TIM HALL (Private Tim Hall)
Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine
(I originally learned Arginine was one of them. Oh well, I'm not changing my mnemonic device now.) |
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Term
| Why are some amino acids conditionally essential? |
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Definition
| They are required in young, growing animals and/or during illness. |
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Term
| Why are Cysteine and Tyrosine almost considered essential? |
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Definition
Cysteine relies on Methionine for synthesis
Tyrosine relies on Phenylalanine
(Met and Tyr are essential) |
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Term
| Why is a low pH required to begin protein degradation? |
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Definition
| So the protein will denature into a linear form, more susceptible to hydrolysis |
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Term
| Why is it important to have inactive zymogens instead of already active enzymes? |
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Definition
| The enzymes could degrade the pancreas or stomach if they weren't controlled |
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Term
| What does pepsin hydrolyze? |
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Definition
| Leucine, aromatic AAs, acidic AAs |
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Term
| What activates trypsin from trypsinogen? |
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Definition
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Term
| What precursors does trypsin activate? |
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Definition
| Itself (positive feedback), chymotrypsin, carboxypeptidases, elastase |
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Term
| What specificity does Trypsin cleave? |
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Definition
C-terminal of Arg or Lys
(positive/basic amino acids) |
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Term
| What specificity does Chymotrypsin cleave? |
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Definition
C-terminal side of Trp, Tyr, and Phe
(Aromatic residues) |
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Term
| What specificity does elastase cleave? |
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Definition
| C-terminal of small amino acids |
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Term
| What specificity does Carboxypeptidase A cleave? |
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Definition
| The terminal residue IF the last residue is aromatic or aliphatic |
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Term
| Define aliphatic amino acid |
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Definition
Nonpolar, carbon-only amino acids
Gly, Ala, Val, Leu, Ile, Pro |
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Term
| What specificity does Carboxypeptidase B cleave? |
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Definition
| The terminal residue IF the residue is Arg or Lys |
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Term
| What are the proteases on the intestinal cell lining? |
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Definition
Aminopeptidases (cleaves N-terminal AA)
Carboxypeptidases (cleaves C-terminal AA) |
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Term
| Describe amino acid absorption in the small intestine |
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Definition
| Very rapid, active transport mechanisms, specific transport systems, similar amino acids compete for absorption |
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Term
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Definition
| Defect in reabsorption of dibasic amino acids, causes kidney stones made of cystine |
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Term
| What is the treatment for Cystinuria? |
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Definition
| Increases fluid intake and alkanization of the urine above pH 7.5 (oral potassium citrate is taken) |
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Term
| Define dibasic amino acid |
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Definition
Amino acids with a +2 charge under acidic conditions
(They would have an NH3 in the side group) |
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Term
| List the dibasic amino acids |
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Definition
| Lysine, Arginine, Ornithine, Cystine |
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Term
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Definition
| 2 cysteines with crosslinked side chains |
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Term
| What are the two stages of degradation of cellular proteins? |
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Definition
1. Ubiquitination
2. Proteasome digestion |
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Term
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Definition
| 4 ubiquitin molecules attach on the protein to be degraded through a multi-enzyme reaction |
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Term
|
Definition
A small protein present in all cells that mark protein to be degraded.
76 units long each, so 4 are very noticeable for |
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Term
|
Definition
| A trashcan-shaped barrel that degrade proteins attached to polyubiquitin |
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Term
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Definition
| A rule that states that a protein's half-life is related to it's amino-terminal amino acid |
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Term
| Why would some proteins have a half-life of only 2 minutes? |
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Definition
| Ex. neuropeptides that would need to be degraded rapidly |
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Term
| What is the first step to breakdown amino acids? |
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Definition
| Removing the α-amino group |
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Term
| What are the two major mechanisms involved in removing the α-amino group |
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Definition
1. Transamination
2. Oxidative deamination |
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Term
| Describe the passage of the ammonia group in transamination |
|
Definition
1. Transfer from L-Amino Acid to PLP
2. PLP is now PMP
3. PMP transfer to α-Ketoglutarate
4. α-Ketoglutarate is now L-Glutamate |
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Term
| What do PLP and PMP stand for? |
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Definition
PLP- pyridoxal phosphate
PMP- pyridoxamine phosphate
(enzymes in transamination) |
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Term
| What does alanine aminotransferase reversibly catalyze? |
|
Definition
| The transamination of alanine, forming glutamate and pyruvate |
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Term
| What does aspartate aminotransferase reversibly catalyze? |
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Definition
| The transamination of aspartate to glutamate and oxaloacetate |
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Term
| What happens to the L-glutamate after transamination? |
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Definition
| In the liver, it reversibly undergoes oxidative deamination |
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Term
| What enzyme makes L-glutamate undergo reversible oxidative deamination back to α-Ketoglutarate? |
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Definition
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Term
| What are some regulators of glutamate dehydrogenase? |
|
Definition
ATP or GTP inhibits, ADP or GDP activates
(would make sense so more α-Ketoglutarate could be formed for Krebs cycle) |
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Term
| Why is NH4+ toxic to the body? |
|
Definition
1. It depletes α-Ketoglutarate, inhibiting Krebs cycle, inhibiting ATP formation
2. It depletes glutamate, lowering GABA formation, harming the CNS |
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Term
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Definition
| Liver ONLY. One of the reasons why liver damage is so bad. |
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Term
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Definition
| The major form of NH4+ disposal, soluble non-toxic compound excreted in the urine |
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Term
| How many high energy phosphate bonds are needed for the urea cycle? |
|
Definition
4
(2 ATP -> ADP and 1 ATP -> AMP) |
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Term
| What is the first enzyme to incorporate NH4+ into the urea cycle? |
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Definition
| Carbamoyl phosphate binds CO2 and NH4+ into Carbamoyl Phosphate |
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Term
| What enzyme converts Carbamoyl phosphate and L-Ornithine into L-Citrulline? |
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Definition
| Ornithine trans-carbamoylase |
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Term
| What molecules in the urea cycle can pass back and forth from the matrix to the cytosol? |
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Definition
| L-Citrulline and L-Ornithine |
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Term
| Once L-Citrulline crosses into the matrix, what does it bind with? |
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Definition
| L-aspartate, to form Arginosuccinate |
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Term
| What catalyzes the binding of L-Citrulline and L-Aspartate (forming Arginosuccinate)? |
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Definition
| Arginino succinate synthase |
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Term
| What is Arginosuccinate essentially composed of? |
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Definition
| An arginine and an aspartate |
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Term
| What is L-arginine essentially composed of? |
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Definition
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Term
| What is arginosuccinate broken down into by arginosuccinase? |
|
Definition
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Term
| What enzyme converts L-arginine to urea and L-ornithine? |
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Definition
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Term
| What are the two enzymes that require ATP in the urea cycle? |
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Definition
| Carbamoyl phosphate synthetase I and Arginosuccinate synthetase |
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Term
| How is the Urea cycle regulated? |
|
Definition
After a protein-rich meal, glutamate and arginine active N-acetylglutamate synthase.
N-acetylglutamate activates carbamoyl phosphate synthetase 1 |
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|
Term
| What is the rate-limiting step of the urea cycle? |
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Definition
| The first reaction, catalyzed by carbamoyl phosphate synthetase I |
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Term
| What condition results from genetic defects in the Urea cycle? |
|
Definition
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Term
| What are the symptoms of hyperammonemia? |
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Definition
| Tremors, slurring of speech, and blurred vision (due to CNS issues) |
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Term
| What are the two types of hyperammonemia? |
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Definition
| Acquired (from liver damage) and hereditary (genetic defects in urea cycle enzymes) |
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Term
| What are the two treatments for hyperammonemia? |
|
Definition
1. Low protein diet
2. Alternate pathways for nitrogen excretion (more short-term treatment) |
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Term
| Describe how one would treat hyperammonemia by providing alternate pathways for nitrogen excretion |
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Definition
| Sodium benzoate and phenylacetate are given to the patient to push normal, nitrogen-eliminating reactions forward |
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Term
| How does benzoate provide a pathway to remove nitrogen without the urea cycle? |
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Definition
| Benzoate binds to glycine to form Hippurate, which is then excreted in the urine |
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Term
| How does phenylacetate provide a pathway to remove nitrogen without the urea cycle? |
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Definition
| Phenylacetate binds to glutamine to form phenylacetylglutamine, which is then excreted in the urine |
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