BIOL301 Class 16

Question 1

amino acid catabolism in mammals

Answer 1

ammonium can be removed and used to generate other nitrogenous compounds, but excess must be detoxified as urea and removed; the carbon skeletons can be used for energy or other biosynthetic needs

Question 2

nitrogen balance

Answer 2

n intake - n loss = nitrogen balance
- nitrogen balance is measured by assessing dietary N intake vs urinary N output (urea)

Question 3

Positive N balance

Answer 3

childhood growth, pregnancy, muscle building, healing
- nitrogen flowing into the system through anabolism

Question 4

Negative N balance

Answer 4

illness, uterine resorption, starvation, amino acid deficiency, wounding
- nitrogen being lost from the system through catabolism and excreted as urea

Question 5

what happens to “excess” AA’s

Answer 5

they are fed into degradation pathways, leading to excretion of Nitrogen via the UREA CYCLE

Question 6

dietary intake

Answer 6

proteins entering the digestive tract are degraded by proteases and the released amino acids are absorbed into the blood through the intestinal mucosa

Question 7

amino acid absorption

Answer 7

free amino acids generated during digestion are co-transported with Na+ across the intestinal epithelium into the serum
- co transport with oligopeptides
- facilitates transport: high concentration to low concentration

Question 8

what is a “limiting” amino acid

Answer 8

an essential amino acid that is present in insufficient amounts to support protein synthesis
- synthesis of any protein that requires it will stop
- 3/3 amino acids must be present for example

Question 9

protein-energy malnutrition (PEM or Kwashiorkor)

Answer 9

• a diet with excessive calories from non-protein sources such as starch or sugar, but deficient in total protein or essential amino acids
• once common in sugar cane workers

Question 10

marasmus

Answer 10

caloric malnutrition caused by a diet deficiency in both protein and carbohydrates (starvation)

Question 11

kwashiorkor

Answer 11

severe protein deficiency in diet
- the body is nitrogen starved and unbalanced
- multiple “limiting” AA’s
- there are not sufficient AA’s available to regenerate proteins that are degraded (nitrogen balance is giong negative)

Question 12

why do you see edema and dermatitis in someone with kwashiorkor?

Answer 12

you see swelling (edema) because there’s not enough protein to keep fluid inside blood vessels. You also see skin problems (dermatitis) because the skin doesn’t have enough protein to stay healthy and protect against damage.

Question 13

why is kwashiorkor reversible in adults but can cause permanent brain damage in children?

Answer 13

brain changes, undergoing mental development (brain is changing)

Question 14

recycling amino acids; intracellular protein turnover

Answer 14

liver: 70% of the total protein synthesized is turned over every 4-5 days
pancreas: 25% of the total protein synthesized is secreted each day

Question 15

what marks proteins for destruction?

Answer 15

ubiquitin is a peptide that tags cellular proteins for destruction OR can add a recognition site for interaction with other proteins in complex assembly
- 76 AA protein

Question 16

tagging of protein with ubiquitin is a highly regulated process

Answer 16

• E1/E2 ligases perform sequential transfer of Ub to each other and then to an E3 ligase which adds it to the target protein
• the E1/E2 steps are non-specific but the E3 ligase is the one that targets specific proteins

Question 17

the human genome encodes almost 400 E3 ligase genes why so many?

Answer 17

source os specificity, a form of regulation

Question 18

HPV virus

Answer 18

• the E6 protein of the HPV virus activates a specific E3 enzyme that targets Ub to the tumor suppressor protein p53, leading to its degradation
• 90% of all cervical carcinomas show activation of this E3 ligase

Question 19

why would degradation of p53 promote cancer?

Answer 19

p53 normally stops damaged cells from dividing uncontrollably. When p53 is degraded, cells can grow out of control, leading to cancer.

Question 20

glucogenic amino acids

Answer 20

Glucogenic amino acids are those that can be converted into intermediates of the gluconeogenesis pathway, ultimately leading to the synthesis of glucose. During protein synthesis, certain amino acids are designated as glucogenic because they can be broken down into intermediates such as pyruvate, oxaloacetate, or α-ketoglutarate, which can then enter the gluconeogenesis pathway and be converted into glucose. Examples of glucogenic amino acids include alanine, serine, glycine, and glutamine

Question 21

keterogenic amino acids

Answer 21

Ketogenic amino acids are those that can be converted into ketone bodies through the process of ketogenesis. During protein synthesis, certain amino acids are designated as ketogenic because they can be broken down into acetyl-CoA or acetoacetate, which serve as precursors for ketone body synthesis. Ketone bodies, such as acetoacetate, β-hydroxybutyrate, and acetone, can be utilized as alternative fuels by tissues such as the brain and skeletal muscles. Examples of ketogenic amino acids include leucine, lysine, and isoleucine.

Question 22

mobilization of proteins for energy during fasting/starvation

Answer 22

• the liver plays a central role in maintaining nitrogen balance: when nitrogen balance is negative, its role is critical

Question 23

alanine and glutamate play essential roles in nitrogen mobilization and metabolism

Answer 23

• glucose alanine shuttle: as protein from muscle is degraded for fuel; NH4+ is stripped out to glutamate and then to alanine
• alanine carries NH4+ to the liver where it is transferred back to Glu and then detoxified in the UREA CYCLE
• the pyruvate generated by aminotransferase rxn can be used for gluconeogenesis

Question 24

high protein/low carb diets trigger glucagon signaling/gluconeogenesis

Answer 24

high carb meal
- high glucose
- high insulin
- high glucagon
high protein meal
- stable nitrogen
- stable glucose
- small peak insulin
- high ongoing glucagon

Question 25

high protein/low carb diets are observed to cause high energy expenditure why would this happen?

Answer 25

In low-carbohydrate diets, the body may rely more on gluconeogenesis, a process where the liver produces glucose from non-carbohydrate sources such as amino acids (derived from proteins). This process requires energy, contributing to increased energy expenditure.

Question 26

nitrogen excretion

Answer 26

• when the carbon skeleton is needed, nitrogen is stripped out as NH4+, a substance toxic to the cell
• in terrestrial vertebrates, NH+ is detoxified into urea in the liver through the Urea Cycle for excretion

Question 27

Urea Cycle

Answer 27

• Ornithine plays a role similar to Oxaloacetate in the TCA cycle; it is the initial ammonia acceptor and is regenerated with a full turn of the cycle
• only one carbon is excreted per 2 NH3’s in the urea cycle

Question 28

Glutamine Synthetase

Answer 28

• NH4+ in all tissues can also be detoxified for transport to the liver as glutamine using glutamine synthetase where it is removed in the mitochondria by glutaminase
• the glutamate produced by glutaminase can be further deaminated by glutamate dehydrogenase

Question 29

vertebrate liver

Answer 29

the liver is the distribution manage of the vertebrate system
- excess nitrogen/NH3 is brought there in the form of amino acids, stripped out, and then couples to CO2 to form urea for excretion
- carbons are reused to form energy supplies for other tissues (glucose and ketone bodies)

Question 30

The UREA CYCle

Answer 30

1) formation of citrulline from ornithine and carbomoyl phosphate in the mitochondria: citrulline is transported into the cytoplasm
2) formation of energized citrulline by AMP; replacement of AMP by aspartate to create arginosuccinate
3) cleavage of arginosuccinate into arginine and fumarate
4) cleavage of arginine into urea and ornithine, which can then go back into the mitochondria for another round of urea synthesis
- only a single carbon is lost to the environment while carrying 2 NH2’s

Question 31

Carbomoyl-Phosphate Synthetase I (CPS-I)

Answer 31

• the commitment step in the urea cycle
• allosterically activated by N-acetylglutamate which is synthesised when cellular glutamate is up, signaling an excess of free AA’s OR amino acid catabolism
• note energy cost of detoxifying NH3
• confined to LIVER mitochondria in mammals; constitutes 15-26% of total mitochondrial matrix protein in liver cells

Question 32

Regulation of the Urea Cycle

Answer 32

1) high protein diet or starvation yields high NH4+ concentration, increasing the need for the urea cycle
2) more long-term controls include upregulation of the genes encoding the urea cycle enzymes
3) shorter term control utilizes the synthesis of an allosteric activator of CPSI: N-acetylglutamate

Question 33

high levels of glutamate, and arginine allosterically activate N-acetylglutamate synthase - why does this make sense? what does increased arginine and glutamate levels in the liver indicate?

Answer 33

Glutamate: Think of glutamate as a helpful ingredient in a recipe. In the body, it helps make a substance called N-acetylglutamate (NAG), which is like a key ingredient for a machine (enzyme) that helps clean out waste.
Arginine: Arginine is another key ingredient in the body’s waste-cleaning machine. When there’s a lot of arginine around, it tells the machine to work efficiently.

Question 34

The urea cycle has both mitochondrial and cytoplasmic reactions

Answer 34

aspartate is condensed with citrulline in the cytosol so the urea cycle needs cytoplasmic aspartate

Question 35

Defects in the urea cycle enzymes all cause hyperammonemia (excess Nh4+), leading to a variety of CNS malfunctions, including coma and seizures. why is ammonium so toxic to the brain?

Answer 35

Ammonium interferes with neurotransmission, the process by which nerve cells communicate with each other. It disrupts the balance of neurotransmitters, such as glutamate and gamma-aminobutyric acid (GABA), which are essential for normal brain function. Excess ammonium can lead to increased levels of excitatory neurotransmitters like glutamate, which can overstimulate nerve cells, leading to neuronal damage and dysfunction.

Question 36

the resulting depletion of alpha ketoglutarate could impair energy production in the brain.. how? why is the brain mostly affected? why is the brain so sensitive to low O2 levels?

Answer 36

When alpha-ketoglutarate levels are low, energy production in the brain is impaired because it’s a crucial component in the process that generates energy. The brain is especially vulnerable because it relies heavily on glucose and oxygen for energy, has high metabolic demands, and can’t store glucose. Low oxygen levels further exacerbate the issue by hindering aerobic respiration, the brain’s primary energy source. In essence, any disruption in energy supply, like low alpha-ketoglutarate or oxygen, significantly impairs brain function.