UNIT IV Nitrogen Metabolism

Question 1

Overview Amino Acids: Nitrogen Disposal

1. TRUE or FALSE: amino acids stored in the body in the same sense as carbs and fat?
2. Mention a few ways on how to obtain amino acids ?
3. name the first phase of amino acid catabolism
4. name another phase of amino acid catabolism other than number 3
5. what is the fate of any amino acid in excess in body needs of the cell ?

Answer 1

1. FALSE: amino acids are NOT stored- no protein exists whose whole function is to maintain a supply of amino acids for future use.
2. from diet, de novo syntheses or produced from the degradation of body protein
3. Transamination mechanism
4. oxidative deamination
5. they are rapidly degraded

Question 2

1. In the first phase of amino acid catabolism; what is being REMOVED ?
2. when the alpha amino group is removed, what does it form ?
3. what is the small portion in this mechanism is secreted in the urine
4. most of the ammonia and not small parts are used in the formation of what ?

Answer 2

1. alpha - amino group
2. ammonia and alpha keto acid (the carbon skeleton of the amino acid)
3. a portion of free ammonia
4. urea

Question 3

Overall Nitrogen Metabolism

1. TRUE or FALSE ? Amino acid catabolism is part of the larger process of the metabolism of “nitrogen-containing” molecules.
2. what does nitrogen leave the body as ??
3. TWO concepts to grasp in the transformations of these proteins are ?

Answer 3

1. TRUE
2. ammonia and urea; also as creatine
3. amino acid pool protein turn over

Question 4

Amino Acid Pool

1. what are the three sources that make up the pool of amino acids ?
2. what are the three routes that DEPLETE the pool of amino acids ?
3. compared to the amount of protein in the body how will you describe the amount of amino acid pool ?

Answer 4

• degradation of endogenous (body) proteins (reused)
• exogenous (dietary) proteins
• nonessential amino acids synthesized from simple intermediates of metabolism
• formation/ syntheses of body proteins
• consumption of A.A. as precursors of essential nitrogen-containing molecules
• conversion of A.A. to glucose, glycogen, fatty acids, and ketone bodies or OXIDATION to CO2 + H2O

IT IS smaller compared to the proteins in the body

90- 100 g of amino acids pool < 12 kg in a 70 kg man for proteins in the body

Question 5

1. The simultaneous synthesis and degradation of protein molecules ?
2. total amount of proteins in a healthy body remains constant because ?
3. what is controlled by selective degradation

Answer 5

1. protein turn over
2. the rate of protein synthesis is exactly enough (sufficient) to replace the protein that is degraded
3. cellular proteins

Question 6

What are the two major enzyme systems responsible for degrading proteins ?

Answer 6

1. ATP- dependent Ubiquitin (Ub)-proteasome complex/ system (cytosol)
2. ATP -independent degradative system (lysosomes)

Question 7

define the following terms below

1. proteasome
2. lysosome
3. acid hydrolase
4. autophagy
5. heterophagy

Answer 7

1. selective- degradation “damaged” and or “short-lived proteins
2. nonselective - degradation of “intracellular” proteins (plasma proteins)
3. Lysosomes use hydrolase to destroy proteins
4. destroying proteins intracellularly (autophagy)
5. destroying proteins extracellularly (heterophagy)

Question 8

Ubiquitin–Proteasome System

1. What is ubiquitin ?
2. How many steps does ubiquitination process involve ?
3. ubiquitination of the target substrate occurs through what type of linkage ?
4. what are the enzymes involved in the three step process
5. is the process ATP-dependent or ATP-independent ?

Answer 8

1. a small globular non-enzymatic protein in eukaryotic species.
2. three steps
3. isopeptide linkage of the ALPHA - carboxyl group of the C-terminal GLYCINE of Ub to the OMEGA- group of the LYSINE
4. E1 E2 and E3
5. ATP-dependent (needs ATP)

Question 9

E1, E2 and E3 of the ubiquitination steps

1. what is the job of enzyme 1
2. what is the job of enzyme 2
3. function of enzyme 3 : key ligase
4. another function of E3
5. ratio of these Enzymes; which one of them have the most ?

Answer 9

1. activating enzyme
2. conjugating enzyme
3. ligase (identifies the protein to be degraded)
4. interacts with E2-Ub
5. E3 proteins are more than E1 and E2

Question 10

1. what is a polyubiquitin chain ?
2. what does a proteasome do in this mechanism ?
3. Describe a proteasome
4. another term for unfolding
5. deubiquitinated target protein are further degraded by ?
6. where do degraded proteins go after being cut by the proteasome ?

Answer 10

1. consecutive addition of FOUR or more Ub molecules to the target protein
2. it recognizes target proteins tagged with Ub
3. large, barrel-shaped, macromolecular proteolytic complex
4. deubiquinitate; cut into fragments
5. by cytosolic proteases to amino acids
6. goes into the amino acid pool

Question 11

1. Degradation signal (describe this in 4 points)
2. what is the N-rule
3. what are the destabilizing and stabilizing N-terminal amino acids
4. which proteins are rapidly degraded (key) PEST

Answer 11

• proteins have different half-lives
• degradation cannot be random
• degradation signal is influenced by structure aspect
• degradation signal is done and recognized by E3
• half life of a protein is determined by the influence of the N-terminal

1. Destabilizing: Arginine and acylated Alanine
2. Stabilizing: Serine

• proline, glutamine, Serine and threonine (short half lives)