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BIOC 385 - Exam 3 || A+ Graded Already.
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Describe the function of the E1, E2, and E3 enzymes in the ubiquitinating system. Why are there ~500 E3 genes in the human genome but only two E1 genes? correct answers E1 enzymes attached ubiquitin to E2 enzymes, E2 enzymes conjugate ubiquitin to target proteins, and E3 enzymes recognize target pr...

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  • August 20, 2024
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  • 2024/2025
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  • describe the function of the e1 e2 and e3 enzyme

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BIOC 385 - Exam 3 || A+ Graded Already.
Describe the function of the E1, E2, and E3 enzymes in the ubiquitinating system. Why are there
~500 E3 genes in the human genome but only two E1 genes? correct answers E1 enzymes
attached ubiquitin to E2 enzymes, E2 enzymes conjugate ubiquitin to target proteins, and E3
enzymes recognize target proteins and facilitate ubiquitination by interacting directly with E2-
ubiquitin and the target protein. E3 proteins must recognize a large number of target proteins,
and thus there are hundreds of different E3 genes. In contrast, E1 needs to recognize only
ubiquitin and E2 and therefore fewer genes are needed.

What is the metabolic function of the "Krebs bicycle" in nitrogen metabolism? correct answers
The Krebs bicycle is a set of reactions that link the urea cycle and citrate cycle through fumarate.
This shunt pathway recycles the carbon backbone of aspartate, which donates one of the two
nitrogen to urea. Fumarate produced by the urea cycle is used by the citrate cycle to generate
oxaloacetate for the aspartate aminotransferase reaction. In this way, the amino group of
glutamate is transferred to urea via aspartate and fumarate.

What is the difference between a glucogenic and ketogenic amino acid? Which amino acids fit
the description of both a glucogenic and ketogenic amino acid? correct answers Glucogenic
amino acids are metabolized to form pyruvate or citrate cycle intermediates, precursors for
gluconeogenesis. Ketogenic amino acids are converted into acetyl-CoA or acetoacetyl-CoA,
which give rise to ketone bones.

Isoleucine, phenylalanine, threonine, tyrptophan and tyrosine are both glucogenic and ketogenic

What is the functional definition of essential and nonessential amino acids in the human diet?
How might this functional definition be explained in evolutionary terms? correct answers
Essential amino acids: must be obtained in our diet because we lack necessary enzymes for their
synthesis.

Nonessential amino acids: we can synthesize and do not necessarily need in our diets.

As plants and bacteria must be able to synthesize all 20 amino acids for survival, but humans eat
diverse foods that provide many amino acid requirements, an evolutionary explanation is humans
have lost the amino acid biosynthetic pathways that require multiple steps and are the most
complex and energy demanding; that is, pathways for the 10 essential amino acids

When 15N-labeled aspartate is fed to animals, many 15N-labeled amino acids appear in protein
within a short time.

a) explain this observation and include in your answers the most likely enzyme reactions
responsible for this finding

b) What is the enzyme cofactor in this reaction, and what type of chemical bond must be formed
for the reaction to proceed? correct answers a) Aspartate is a common amino group donor for
transamination such as:

,Aspartate + a-keto acid >> Oxaloacetate + a amino acid

Because the a-keto acid in the equation can come from any amino acid, the 15N from aspartate is
rapidly transferred to other amino acids

b) The cofactor is pyridoxal phosphate, which forms a Schiff base between the cofactor carbonyl
carbon and an amino group from either a lysine of the enzyme or a free amino acid

Cats were fasted overnight and then given a single meal containing all amino acids except
arginine. Within 2 hours, blood ammonia levels rose by 800%. A control group of cats were
fasted and then fed the same meal but with arginine included, and showed no change in blood
ammonia levels.

a) Fasting was required to obtain this difference in blood ammonia levels. Why?

b) What caused the ammonia levels to rise in the experimental group compared to the control
group? correct answers a) Fasting lowered blood glucose, so that the fed amino acids are
deaminated to form substrates for gluconeogenesis

b) Arginine is required for the urea cycle thus the experimental animals were unable to remove
ammonia via the urea cycle

Why does it make metabolic sense that tadpoles (which live in water) have low levels of the
enzyme arginase, but after their metamorphosis into frogs (which spend extended periods of time
on land) their arginase levels increase dramatically? correct answers Tadpoles can excrete
ammonia directly into the water, but frogs that live on land need to converse water and excrete
ammonia as urea. Arginase is essential for the production of urea from arginine.

A newborn infant with highly elevated levels of blood ammonia was diagnosed to have a urea
cycle enzyme defect in either carbamoyl phosphate synthetase or arginase. The clinical lab was
able to measure the concentrations of alanine, glutamine and arginine in the blood, but enzyme
assays were not available. How would knowledge of abnormal levels of alanine, glutamine or
arginine in the blood be useful to distinguish between an enzyme defect in carbamoyl phosphate
synthetase or arginase? correct answers An enzyme defect in carbamoyl phosphate synthetase
would block the urea cycle at the the first step of citrulline production from ornithine and
carbamoyl phosphate. This would cause higher than normal alanine and glutamine
concentrations because they cannot be metabolized and lower than normal arginine concentration
because the urea cycle is not functioning (no arginine produced or argininosuccinase). However,
a defective arginase would cause arginine to accumulate , and alanine and glutamine
concentrations would be closer to normal, assuming excess nitrogen is excreted as
argininosuccinate and arginine.

Individuals with enzyme deficiencies in the urea cycle have elevated blood ammonia levels,
which can be life threatening. One useful therapy is to feed these individuals benzoic acid, which
reacts with glycine to form hippuric acid. This compound can be excreted in urine. Why does

, benzoic acid therapy lower blood ammonia levels in these individuals? correct answers An
alternative way to excrete nitrogen-rich products is glycine-depletion by formation of hippuric
acid. This process drives ammonia into amino acid synthesis reactions to replace the lost glycine,
thereby lowering the level of free ammonia.

All 20 amino acids are found in the bloodstream, but alanine and glutamine are by far the most
abundant. Explain this observation. correct answers Glutamine carries nitrogen from most tissues
to the liver for disposal after transamination reactions, whereas alanine carries nitrogen from
muscle to the liver. The alanine-glucose cycle is responsible for removing excess muscle
nitrogen that is due to protein degradation.

Kwashiorkor is a dietary deficiency disease characterized by decreased pigment in the skin and
hair

a) which major food group is likely missing from the diet?

b) what would you conclude if adding the missing food group to the diet had no effect on the
skin and hair condition? correct answers a) Kwashiorkor is caused by a lack of protein in the
diet. The decreased pigmentation is caused by a deficiency in tyrosine, which is the precursor to
melanin pigments. Moreover, because phenylalanine is converted to tyrosine by phenylalanine
hydroxylase, phenylalanine deficiency also contributes to the skin and hair condition.

b) In this case, the individual may have a defect in an enzyme required to convert tyrosine to
melanin.

Individuals with the disease phenylketonuria lack the enzyme phentylalanine hydroxylase, which
is required to convert phenylalanine to tyrosine. Albinism is a disease characterized by lack of
skin pigments due to a deficiency in the enzyme tyrosinse.

a) explain why patients with PKU can be spared from many of the deleterious effects of the
disease, whereas there is no feasible treatment for albinism?

b) Explain why individuals with PKU are not complete albinos, even though they cannot
synthesize tyrosine from phenylalanine. correct answers a) The level of phenylalanine in the
body can be controlled by diet. There is no safe way to continually add pigments to the cells
through diet or drugs.

b) Individuals with PKU have tyrosinase and obtain tyrosine in their diet.

Nucleotide salvage pathways are an important recycling process in cells because they require
less ATP than the de novo biosynthetic pathways use. What is the source of most nucleotide
bases salvaged by recycling processes in cells? correct answers The degradation of cellular RNA,
a transient nucleic acid required for gene expression. Because RNA doesn't contain thymine,
salvaged dTMP (thymidylate) from DNA is the only source of thyme and thymidine

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