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Homework 2, 4, 6, 9, 13. Ubiquitin is a small protein (76 aa) used as a marker for
cellular protein turnover. Marked proteins are unfolded and broken down by the
proteasome, a "garbage can" shaped structure which is related to Gro-EL, a
folding chaperone (the opposite job!). Dietary protein is hydrolyzed by pepsin in
the stomach, and then by trypsin, chymotrypsin, and other proteases in the small
intestine. Essentially all protein consumed orally is broken down to amino acids,
which is why money spent on most "enzyme pills" (like Superoxide Dismutase) is
Amino acid catabolism starts with transamination. Amino groups are transferred
to alpha-ketoglutarate by specific aminotransferase enzymes (656). The resulting
glutamate is then oxidatively deaminated by glutamate DH which can use either
NAD+ or NADP+. The ammonia produced is generally incorporated into urea for
excretion. Ammonia is toxic if allowed to build up. You should understand how
PLP, pyridoxal phosphate works. PLP is the cofactor for very many amino acid
reactions. Aspartate aminotransferase is presented as an example in the text
(659-660). Understand that the group that is perpendicular to the plane of PLP is
the group that is removed. [The old name for Asp Amino Trans was Glutamate
Oxaloacetate Transaminase or "GOT." Doctors still prescribe blood tests for
SGOT – S for serum – as an indicator of heart or liver damage.] Serine breaks
down two ways – serine dehydratase deaminates to form pyruvate, and serine
hydroxymethyltransferase reversibly produces glycine. Know that alanine and
glutamine can carry nitrogen through the blood from muscles to liver, where excess
nitrogen enters the urea cycle.
Know the complete Urea Cycle, with synthesis of carbamoyl phosphate (661-3).
Understand the connection to the Citric Acid Cycle. The discussion of the
evolution of the urea cycle is interesting. In fact "Aspartate donation" as shown
on 664 is one of the major modes of nitrogen transfer, along with "Glutamine
donation," Transamination and formation/attachment of Carbamoyl Phosphate.
What are glucogenic and ketogenic amino acids? (Fig. 23.22). Know the three,
four, and five carbon families of amino acids (on 667-9) and be able to show the
breakdown of proline or arginine to glutamate, as shown in class. Know the
pathway from phenylalanine to epinephrine (on handout). This starts with Phe
Hydroxylase (671) the lack of which causes PKU or Phenylketonuria (673).