Making/Breaking Amino Acids

Question 1

How does nitrogen enter the body?

Answer 1

Through the protein in the foods we eat

Question 2

How does nitrogen exit the body?

Answer 2

Through the urea in our urine

Question 3

What is the amino acid pool?

Answer 3

The total amount of free amino acids available at any time in the body

Question 4

What are the ways amino acids are added to the amino acid pool?

Answer 4

1. Dietary protein
2. Degradation of body proteins
3. Synthesis of nonessential amino acids

Question 5

What are the ways that the amino acid pool is depleted?

Answer 5

1. Synthesis of body protein
2. Consumption of amino acids as as precursors for nitrogen-containing molecules
3. Conversion of amino acids to glucose/glycogen/fatty acids/ketone bodies/CO2+H2O

Question 6

What are the systems that degrade unused proteins?

Answer 6

1. Ubiquitin-proteasome system
2. Lysosomal degradation system

Question 7

Which protein degradation pathway uses ATP?

Answer 7

Ubiquitin-proteosome system

Question 8

What is the ubiquitin-proteasome pathway made of structurally?

Answer 8

One alpha helix and beta sheets

Question 9

What is ubiquitination? (General)

Answer 9

Proteins are selected and tagged with a ubiquitin molecule to be taken up and degraded by proteosome molecules

Ubiquitin uses ATP to bind to the amino group of a protein again and again to make a polyubiquitin chain that attracts a proteasome that acts as a garbage disposal to denatures and removes the ubiquitin form the protein so that it can be further broken down.

Question 10

What does the proteasome complex do?

Answer 10

Recognizes the polyubiquitin chain on the amino acids of proteins, denatures to proteins, and break down the protein into amino acids

Question 11

What does ubiquitin do?

Answer 11

Tags the amino acids of proteins to be recognized by proteasomes for degradation

Question 12

What are the enzymes of the ubiquitination system?

Answer 12

1. ubiquitin-activating enzyme (E1)
2. ubiquitin-conjugating enzyme (E2)
3. ubiquitin-protein ligase (E3)

Question 13

What are the steps of ubiquitination? (Detailed)

Answer 13

1. Activation: Ubiquitin-activating enzyme E1 uses ATP to bind to ubiquitin and activate it
2. Conjugation: Ubiquitin-conjugating enzyme E2 binds to ubiquitin-E1 complex and transfers the ubiquitin form E1 site to the active site on E2
3. Ligation: Ubiquitin-ligase E3 binds the ubiquitin to the amino acid of the protein

*Ub + ATP –> E1 ==> E1/ub
*E1/[ub] –> ub –> E2 ==> E2/ub
*E2/ub + E3/protein –> E3/protein/ub
*E3/protein/ub - E3 ==> {protein/ub}

Question 14

Describe the proteosome

Answer 14

The proteosome is a barrel-shamed complex with two regulartory particles at the end (unfolds/denatures/straightens out protein strand) and one big core particle with an active site (used ATP to cleave the protein into amino acids). The leftover ubiquitin is recycled for other proteins.

Question 15

What is the Lysosomal degradation pathway?

Answer 15

Lysosomes act as an acid pit that takes up cellular components (in this case, protein) and break them down. This is more random and doesn’t require ATP energy.

Question 15

What is the process of protein digestion? (Gastric)

Answer 15

1. Food (protein)–> Teeth/Saliva
2. Stomach –> HCl (parietal cells) –> denatures proteins
3. Pepsinogen (stomach chief cells) –> [inactive]
4. HCl + pepsinogen ==> pepsin –> [active]
5. Pepsin + proteins ==> Peptides + amino acids

Question 16

Describe gastric protein degradation

Answer 16

Food is broken down mechanically by the teeth and the saliva. The protein is swallowed and ends up in the stomach. The stomach is full of parietal cell HCl, which will kill bacteria and denature the dietary proteins. The chief cells of the stomach will secret inactive pepsinogen which will be activated by HCl into active pepsin. Active pepsin will break the proteins down into polypeptides and amino acids.

Question 16

Digestion of oligopeptides

Answer 16

Oligopeptides in the small intestine are cleaved into amino acids by the intestinal enzyme aminopeptidase

Question 17

Describe pancreatic protein digestion.

Answer 17

Polypeptides and amino acids from the stomach flow down to the small intestine. The the digestive hormone secretin causes the pancreas to secret several enzymes that cleave specific amino acids. The proteases (Trypsinogen, Chymotrypsinogen, Prolastase, Procarboxypeptidase A&B) are inactive in at first, but are transformed into their active forms (Trypsin, Cymotrypsin, Elastase, Carboxypeptidase A&B) by an intestinal enzyme called enteropeptidase. These active enzymes then break the polypeptides down into oligopeptides.

Question 17

What is an inactive enzyme?

Answer 17

Zymogen

Question 17

Describe the absorption of amino acids

Answer 17

Final amino acids in the small intestine are absorbed through the lining of the intestine where they are transported through the portal vein where they either travel to the liver, the bloodstream, or the muscle (branched-chain amino acids)

Question 18

What are branched-chain amino acids?

Answer 18

Essential amino acids that are made of leucine, isoleucine, and valine used to build proteins for muscles

Question 18

What keeps the amino acids in the cells?

Answer 18

There is a concentration of amino acids inside the cell that is maintained by ATP-driven active transport systems

Question 19

What is cystinuria?

Answer 19

Defect in the cell’s uptake of cystine, ornithine, arginine, and lysine (COAL), leading to their presence in urine. This causes kidney stones and can be treated by drinking more water.

Question 20

What is Hartnup disorder?

Answer 20

Defect in the cell’s ability to uptake the amino acid tryptophan, causing pellagra-like symptoms

Question 21

What is the overview of amino acid catabolism?

Answer 21

Amino acids are broken into the amine group and the carbon skeleton. The carbon skeleton is recycled into glucose, acetyle-coa, ketone bodies, CO2 and H2O. The amine groups go into the urea cycle to shuttle toxic ammonia safely out of the body in the form of urine.

Question 22

What is used to make NAD?

Answer 22

Quinolinate (From Tryptophan)