FCH 532 Study Guide
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1. Starting out from ribose-5-phosphate, write out the metabolic pathway for the
production of inosine monophosphate (IMP). Show all chemical structures and
names of substrates. Also show co-factors and enzymes.
a. Continue from IMP to produce AMP and GMP. How is purine synthesis
regulated?
2. Show the pathways for the de novo synthesis of pyrimidines. In what ways does
this differ from purine synthesis.
3 possible pyrimidines U, C, and T.
Pyrimidines are simpler to synthesize than purines. Fewer steps.
N1, C4, C5, and C6 come from Asp
C2 from bicarbonate
N3 from Gln
Start by synthesizing uracil monophosphate (UMP)
After UMP is formed , converted to UTp by nucleoside monophosphate kinase and
nucleoside diphosphate kinase respectively.
UMP + ATP  UDP + ADP
UDP + ATP  UTP + ADP
UTP is converted to CTP by CTP synthetase.
CTP is formed by amination of UTP by CTP synthetase
In animals, amino group from Gln
T is made from dUMP and is more complicated.
•2 main enzymes: dUTP diphosphohydrolase (dUTPase) and thymidylate synthase
Reaction 1
•dTMP is made by methylation of dUMP.
•dUMP is made by hydrolysis of dUTP via dUTP diphosphohydrolase (dUTPase)
dUTP + H2O  dUMP+ PPi
•Done to minimize the concentration of dUTP-prevents incorporation of uracil into
DNA.
Reaction 2
•dTMP is made from dUMP by thymidylate synthase (TS).
Uses N5, N10-methylene-THF as methyl donor
In bacteria, amino group from ammonia
3. How is pyrimidine biosynthesis regulated in E. coli as compared to in animals?
4. What is the function of ribonucleotide reductase? Write out a mechanism for this
enzyme’s reaction.
RNR is necessary to produce deoxyribose derivatives by reducing ribonucleotides at the
C2’ position.
5. Write out a plausible mechanism for the inhibition of thymidylate synthetase by
FdUMP.
H2N
N
H
N
O
N+
CH2
R
CH2
N
HN
O-
O
F
HN
O
:B
H
-S E
dRib-P
N
CH2
H
F
HN
H
S
N
O
:B
E
dRib-P
H2N
N
H
N
CH2
H+ H
N
CH2
O
R
O
CH2
N
F
HN
H
:B
N
O
S
E
dRib-P
HN
6. Write out the major catabolic pathways for purines and pyrimidines. Show all
chemical structures.
See above and notes.
7. Write the pathway for the biosynthesis of uridine triphosphate UTP) naming all
enzymes, coenzymes, and substrates. You should show the structure of all
substrates but need not show the structures of the enzyme intermediates
See above.
8. Briefly discuss the biochemical mechanism by which a cell regulates purine
biosynthesis so it obtains balanced amounts of both purine nucleotides.
In order to achieve balanced amounts of purine nucleotides, the reactions catalyze the
first steps that convert IMP to either AMP or GMP are regulated by feedback inhibition.
Adenylosuccinate synthase which converts IMP to adenylosuccinate is inhibited by AMP
and ADP. IMP dehydrogenase that converts IMP to xanthosine monophosphate (XMP)
is inhibited by GMP and GDP. ATP activates the GMP synthetase which converts XMP
to GMP and GTP activates adenylosuccinate synthase.
9. Most nucleotide bases are reused rather than synthesized from scratch. Briefly
discuss the reutilization pathways for purines and contrast the difference in ATP
requirements to reutilize adenine for the synthesis of ATP versus forming a new
ATP by de novo synthesis.
Free purines such as adenine, guanine, and hypoxanthine can be reconverted to their
corresponding nucleotides through salvage pathways. These are catalyzed by two
enzymes:
Adeninephosphoribosyltransferase (APRT)
Adenine + PRPP  AMP + PPi
and
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
Hypoxanthine + PRPP  IMP + PPi
Guanine + PRPP  GMP + PPi
These require far less energy than synthesizing these molecules from purine biosynthesis
which uses additional 5 ATP molecules vs. the 1 necessary for regenerating PRPP (purine
biosynthesis also uses this ATP to generate PRPP, thus consuming 6 ATP molecules per
nucleotide formed).
10. Inhibitors of one-carbon metabolism (THF) block the synthesis of DNA but not
RNA, why?
N5, N10-Methylenetetrahydrofolate (THF) is an essential cofactor for thymidylate
synthase, the enzyme responsible for the production of dTMP. If THF metabolism is
inhibited, dTMP production is inhibited. Since thymine is essential for DNA synthesis
but not RNA synthesis, only DNA synthesis will be inhibited.
11. Name the different nucleotides, their nucleosides and their component bases.
12. Define the following terms: Z-scheme, photorespiration, photosystem 2, light
harvesting complex, chlorophyll, Calvin cycle, lumen, photoautotroph, Rubisco,
etc.
Z-scheme: describes two-center electron transport. This system uses reding power
derived from light energy to drive the oxidation of water to produce NADPH. It requires
two processes: The first catalyzed by Photosystem II (PSII) that generates a strong
oxidant to oxidize H2O and a weak reductant. The second catalyzed by Photosystem I
(PSI) that generates a strong reductant capable of reducing NADP+.
photorespiration: Illuminated plants can consume O2 and evolve CO2 distinct from
oxidative phosphorylation.
O2 competes with CO2 as substrate for RUBP carboxylase.
O2 reacts with RuBP to form 3PG and 2-phosphoglycolate.
2-phosphoglycolate is hydrolyzed to glycolate by glycolate phosphatase.
Partially oxidized to yield CO2 in peroxisome(aka glyoxisome) and mitochondria.
Dissipates some ATP and NADPH generated by light reactions.
photosystem 2: AKA photosystem II (PSII). An oxygen evolving complex responsible
for the oxidation of of water. Two molecules of ChlA make up P680 is the photon
absorbing center. Absorbance of a photon converts P680 to P680* which then donates
electron to Pheo a which then passes it’s electron to quinones QA and QB and to the
quinone pool. producing P680+ which can return to the original state by removing
electron from TyrZ. TyrZ derives its electrons from the oxygen evolving complex (OEX)
which contains 4 Mn++ ions. It takes 4 photons of light to charge P680+ 4 times to take
2H2O to O2 and 4H+.
light harvesting complex (LHC): Divided into two types in purple photosynthetic bacteria
(LH1 and LH2) are transmembrane proteins that have different spectral and biochemical
properties. LH2 absorbes light at shorter wavelengths than LH1. LH2 passes energy
from photons it absorbs to LH1 which passes them to the reaction center. LH2 binds 24
bacteriochlorphyll a and 8 lycopene molecules. Many are also associated with accessory
pigments that fill the absorption spectra where chlophylls do not absorb strongly.
antenna chlorophyll: Because reaction centers (RCs) can only intercept ~1 photon per
second, antenna chlorophyll perform an essential role in increasing the efficiency of
photosynthesis. These antenna can pass the energy of an aborbed photon by exciton
transfer from molecule to molecule until they reach a reaction center. These LHCs can
transfer the energy to an RC in <10-10 s with an efficiencty of >90%.
Chlorophyll: Primary photoreceptor for photosynthesis is a cyclic tetrapyrrole that differs
from heme in four major ways.
1.Central metal ion is Mg2+ not Fe(II) or Fe(III).
2. Has cyclopentenone ring, (Ring V), fused to pyrrole Ring III
3. Pyrolle Ring IV is partially reduced in chlorophyll a (Chl a) and chlorophyll b (Chl
b). In bacteriochlorophyll Rings II and IV are partially reduced.
4. Propionyl side chain of Ring IV is esterified to tetraisoprenoid alcohol. In Chl a and b
and Bchlb it is phytol.
Calvin cycle: aka reductive pentose phosphate cycle generates GAP from CO2
Lumen: space inside the thylakoid compartment.
Photoautotroph: An organism, that can use energy from sunlight to convert CO2 into
carbohydrate for use in cellular functions.
Rubisco: ribulose-1,5-bisphosphate carboxylase oxygenase enzyme that catalyzes the
first carbon fixation step in the Calvin cycle.
3. One of the classic experiments conducted by Benson, Bassham and Calvin as part
of their elucidation of the pathway of dark carbon fixation was to feed the algae
14
-C labeled carbon dioxide and then degrade the resulting sugars to determine
which carbons are radio-labeled. Indicate which carbons will be radiolabelled in
the following sugars after feeding radioactive carbon dioxide.
See above (red carbons in Figure 24-31)
4. What are the 4 possible routes of dissipation of excitation energy during
phototransfer?
Internal conversion-electronic energy is converted to heat (molecular motion). Occurs
very rapidly (<10-11s) and molecules returned to ground state.
Fluorescence-electronic energy is reduced to ground state by emitting a photon Occurs
slower than internal conversion (~10-8s).
Emitted photon has a longer wavelength (lower energy) than the initially absorbed
photon.
Accounts for 3-6% of light energy absorbed-usually causes red fluorescence.
Exciton transfer (resonance energy transfer)-electronic energy is directly transferred
to nearby unexcited molecules with similar electronic properties
Funnels the light to photosynthetic reaction centers
Photooxidation-light-excited donor molecule is oxidized by transferring an electron to
an acceptor molecule.