Download top408b1_2006

Topics Covered by F. Deis in 694:408
Garrett and Grisham 3rd Ed.
Tuesday April 25, 2006
Chapter 25: Amino Acid Biosynthesis
ONE CARBON METABOLISM is important in this lecture and next. The most important cofactors
for 1-C-M are THF and SAM. Cobalamin, "B-12" is another. Want to know how important 1-C-M is?
Think about the start of Translation (protein synthesis) in eubacteria. What gets sampled?
Amino acids are grouped by G&G into five biosynthetic families. The alpha-KG family (page 823-4,
we did Pro and Arg), the Asp family (page 828, we did Asp, Asn, and Met), the Pyr family (page 834,
we did Ala only), the 3-PG family (page 835, we did Ser, Cys, and Gly), and the Aromatics (page 836,,
we did Phe and Tyr, sort of).
-KG: Proline biosynthesis was done according to Fig 25.20, page 824. Most texts merge the first two
steps into a "Kinase D.H." but learn it as shown here. G.S.A. spontaneously cyclizes, forming a Schiff
base, which can then be reduced to give Pro. The Orn pathway (Fig 25.21, p. 825) is similar in many
ways but the alpha-amino group of GSA is blocked with an Acetyl group to prevent spontaneous
cyclization. After Orn is produced, it can be converted to Arginine using the Urea Cycle.
Asp: Aspartate itself is the product of a simple transamination of OAA (Fig 25.19 p. 821). Asparagine
Synthetase is an example of adenylation, and an example of one of the three major modes of nitrogen
transfer – donation of the R-group N from Glutamine. The process is shown in Fig 25.26 page 830.
Notice the structure of Cystathionine. It is also generated after S-Adenosylmethionine is utilized in
methylation reactions (Fig 25.28 page 833 shows SAM) by reaction of Homocysteine* with Serine to
yield Cysteine. (*High homocys correlates with arteriosclerosis! Box, p. 834)
Pyr: While the Val and Ile pathways are interesting and not too complicated, they were omitted and you
are not responsible for them. All we did in class was Alanine synthesis, by simple transamination of Pyr.
3-PG: The pathway from 3-Phosphoglycerate to Serine is shown in Fig. 25.31 (p. 837). After Ser is
generated, it is easy to get Glycine by using THF, PLP, and Serine Aldolase, which in G&G is called
"Serine Hydroxymethyltransferase" (Fig 25.32 p. 837). It is important to understand the cofactor
Tetrahydrofolate – see handout and DL p. 855 of G&G. There will be many other instances of THF use
covered in the course
Aromatics: The conversion of Phenylalanine to Tyrosine as in Fig 25.38 (843) was emphasized (rather
than direct synthesis of Tyr shown on page 842). Phenylalanine 4-Monooxygenase uses the cofactor
THB or Tetrahydrobiopterin (similar to THF) to deliver electrons from NADPH to oxygen, which
basically makes the energetics much more favorable for ring oxidation. Lack of this enzyme, or of
enzymes related to THB/DHB interconversion, leads to PKU, Phenylketonuria, discussed briefly in box
on 848. If PKU is not detected and treated in infants, they can lose 5 IQ points per 10 weeks and end up
severely retarded. PKU is not terribly uncommon, 1 per 15,000 births in the U.S. The path from Tyr to
DOPA and Dopamine was then discussed (page 1081) – administration of L-DOPA can relieve
dopamine shortages in the brain and can help treat Parkinsonism (rent film "Awakenings" for examples).
Chapter 25: Amino Acid Catabolism
Topics Covered by F. Deis in 694:408
Garrett and Grisham 3rd Ed.
Amino acids are grouped by G&G into five catabolic families: C-3 (Ala, Ser, Cys), C-4 (Asp, Asn), C-5
(Pro, Arg, His, Gln, Glu), Valine (Val, Ile, Met), and Ketogenic (Leu, Lys, Phe, Tyr). The chart (Fig
25.41) on 845 shows the fate of all 20 amino acids. We did brief examples from some families with no
enzyme names or cofactors used:
C-3, Ala is transaminated to Pyruvate, and Ser reacts with Serine Dehydratase which leads to
direct deamination (843).
C-4, Asn reacts with L-Asparaginase to yield NH3 and Asp (845). Asp can then transaminate to
yield OAA or can go to Fumarate via the Urea Cycle . L-Asparaginase has been used to treat a form of
childhood leukemia. When injected, it deprives cells of Asn. This is not harmful to normal cells but can
harm the leukemia cells. AsNase can be treated with PEG, Polyethylene Glycol, to reduce immune
response and turnover .
C-5, The structures for Pro catabolism are the same as those for Pro synthesis. Of course the
enzymes and cofactors are different, but the catabolic enzymes and cofactors are not shown in the book.
Other amino acids with five contiguous carbons include His, Arg, (Orn), Gln, and Glu. (Fig 25.43, 848).
Deis thinks the DL on p. 845 is preposterous.
Chapter 26: Purine Metabolism
We started with the "map" showing metabolic origin of the atoms of the purine ring (like Fig 26.2 but
using Guanine, to make the point that the three "bottom" nitrogens of Guanine all come from
Glutamine). Then, we discussed synthesis of PRPP followed by the Purine de novo pathway (both
shown in Fig. 26.3 p. 856). You should know structures and cofactors. Enzyme and compound names
are less important. After IMP, the de novo pathway branches, and there are mutual controls which keep
levels of AMP and GMP in balance. As shown in Fig 26.5, GTP provides the energy for AMP
synthesis, and ATP provides the energy for GMP synthesis. There are also feedback controls, as shown
in Fig. 26.6.
The drug Azaserine is an irreversible suicide inhibitor of enzymes which catalyze donation of N from the
R group of Glutamine. (Fig 26.4) See homework problem 26:4 and answer in back of book.
Nucleotide metabolism is "tiered" – all processes are specific for mono, di, or triphosphates.
Nucleotides move up and down from level to level with the aid of two sorts of enzymes. The
monophosphates have specific Kinase enzymes (e.g. Adenylate Kinase, Guanylate Kinase) to go to the
diphosphate level, and diphosphates have a generic Kinase (Nucleoside Diphosphokinase) to move up to
the triphosphate level (859-860).
Nucleotide catabolism can lead to free bases which are oxidized to give Xanthine and Uric Acid. This
can cause health problems (including Gout or Lesch-Nyhan Syndrome, Box p. 862), so we need Salvage
Enzymes to react purines with PRPP and "rescue" them. HGPRT and APRT (Fig 26.7) are salvage
enzymes. Most animals have Urate Oxidase (or Uricase) which produces Allantoin (Fig 26.12) but
humans and apes lack this.
Topics Covered by F. Deis in 694:408
Garrett and Grisham 3rd Ed.
Friday April 28, 2006
Chapter 26: Purine Metabolism
Nucleotide breakdown is catalyzed by specific nucleotidases followed by nucleosidases or nucleoside
phosphorylases (961 ff). Look at Fig 26.8 (863). Adenylate and Adenosine break down via Inosine, so
the Adenine nucleus must be deaminated by Adenylate Deaminase or Adenosine Deaminase. Lack of
Adenosine Deaminase causes SCID, Severe Combined Immunodeficiency syndrome (the "boy in the
bubble" disease, Box p. 862) and gene therapy has been used to transfect the gene into a patient.
Adenylate Deaminase, the other enzyme, is used in an Anaplerotic cycle (Fig 26.9, 864).
Chapter 26: Pyrimidine Metabolism
You should learn the de novo synthesis of UMP, shown on 867 (and page 6 of picture handout). Notice
the contrasts to purine synthesis – purines are built as nucleotides, but the pyrimidine ring is first
assembled and then reacted with PRPP. And the "map" of Cytosine is upside down from that of
Guanine, since the top N of Cytosine comes from GlN and the bottom N from Asp. The Carbamoyl
Phosphate is made by C.P. Synthetase II (Fig. 26.14) which uses N from Glutamine. The first step in the
pathway is catalyzed by ATCase or Aspartate Trans Carbamoylase. The sigmoidal activity curve for the
enzyme from E. coli is slid to the left by stimulators (ATP) and to the right by inhibitors (CTP) (not in
book).
Once UMP is built, it must go "up" two "tiers" to UTP via Uridylate Kinase and NDP Kinase. Then it
can react with CTP Synthetase to become CTP (868-9). The nitrogen comes from another Glutamine
donation with ATP hydrolysis. To go from UTP to dTTP, we need to go "down" a tier to UDP, since
only diphosphates can be reduced to 2'-deoxynucleotides. RNR, Ribonucleotide Reductase, has an
interesting 22 structure, and a "deep" active site which reduces NDP's using Cysteine thiols (870 ff).
After the 2'dNDP has been produced, the oxidized disulfides must be reduced by Thioredoxin, which has
the shape of a long "probe" with sulfhydryls near the tip. Then, Thioredoxin is reduced by Thioredoxin
Reductase, which gets its electrons from NADPH (Fig. 26.22 and handout page 5). RNR can produce all
of the various needed 2'deoxynucleotides.
To continue along the pathway to dTTP – having gotten dUDP and dCDP, we must then get to dUMP.
The dUDP pathway goes first up one tier to dUTP, and then down two tiers via dUTPase (an enzyme
which guards against the use of U in DNA synthesis) which produces dUMP and PPi. There is also a
dCDP pathway which goes "down" to dCMP and then deaminates – Fig 26.25 shows both and Fig 26.26
shows the deamination. dUMP reacts, not with a methyl donor, but with N5N10 methylene THF. The
one carbon fragment is reduced as it is delivered, leaving DHF rather than THF (Fig 26.27) and dTMP.
It then must be reduced, and must find another CH2 group. Inhibitors of this process are used in cancer
chemotherapy (Fig 26-28). [And – while we are thinking about nucleotide structures – analogues of
intact nucleotides are used to fight viral infections. See handout, and see Azidothymidine on p. 915.]