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Nitrogenous Bases
Planar, aromatic, and heterocyclic Derived from purine or pyrimidine Numbering of bases is unprimed
Sugars
Pentoses (5-C sugars) Numbering of sugars is primed
Sugars
D-Ribose and 2-Deoxyribose
Nucleosides
Result from linking one of the sugars with a purine or pyrimidine base through an Nglycosidic linkage
Purines bond to the C1 carbon of the sugar at their N9 atoms Pyrimidines bond to the C1 carbon of the sugar at their N1 atoms
Nucleosides
Phosphate Groups
Mono-, di- or triphosphates Phosphates can be bonded to either C3 or C5 atoms of the sugar
Nucleotides
Result from linking one or more phosphates with a nucleoside onto the 5 end of the molecule through esterification
Nucleotides
RNA (ribonucleic acid) is a polymer of ribonucleotides DNA (deoxyribonucleic acid) is a polymer of deoxyribonucleotides Both deoxy- and ribonucleotides contain Adenine, Guanine and Cytosine
Ribonucleotides contain Uracil Deoxyribonucleotides contain Thymine
Nucleotides
Monomers for nucleic acid polymers Nucleoside Triphosphates are important energy carriers (ATP, GTP) Important components of coenzymes
FAD, NAD+ and Coenzyme A
Naming Conventions
Nucleosides:
Purine nucleosides end in -sine
Adenosine, Guanosine
Nucleotides:
Start with the nucleoside name from above and add mono-, di-, or triphosphate
Adenosine Monophosphate, Cytidine Triphosphate, Deoxythymidine Diphosphate
In-Class Activities
Look at the Nucleotide Structures Take the Nucleotide Identification Quiz Be prepared to identify some of these structures on an exam. Learn some tricks that help you to distinguish among the different structures
Nucleotide Metabolism
PURINE RIBONUCLEOTIDES: formed de novo
i.e., purines are not initially synthesized as free bases First purine derivative formed is Inosine Monophosphate (IMP)
The purine base is hypoxanthine AMP and GMP are formed from IMP
Purine Nucleotides
Get broken down into Uric Acid (a purine) Buchanan (mid 1900s) showed where purine ring components came from:
N1: Aspartate Amine C2, C8: Formate N3, N9: Glutamine C4, C5, N7: Glycine C6: Bicarbonate Ion
O C
OOC
2-
O3P O CH2 H H
O H
H OH
C4 C H2N
5
N CH N
Aspartate + ATP
ADP + Pi
HC CH2 COO
N H
C4 C H2N
5
N CH N
OH OH -D-Ribose-5-Phosphate (R5P)
ATP
Ribose Phosphate Pyrophosphokinase
SAICAR Synthetase
AMP
ATP +HCO3
O C
2-
O3P O CH2 H H OH
O H OH
H O
O P O O
O P O O
HC 4 C H2N
5
N CH N
H2N
C4 C H2N
5
N CH N
Ribose-5-Phosphate
5-Phosphoribosyl--pyrophosphate (PRPP)
Glutamate + PPi
H N H2C CH O NH
O C H
O C H2N
AICAR Transformylase
THF
2-
O3P O CH2 H H OH
O H
NH2
C4 C NH
5
N CH N
C HN
H OH
-5-Phosphoribosylamine (PRA)
Glycine + ATP
GAR Synthetase
ADP + Pi
H 2C O
2-
NH2
H N H2C C
N10-Formyl-THF THF
O C N
4
CH O NH
2-
HN HC N
O3P O CH2 H H OH O
C NH H H OH
GAR Transformylase
CH N
H H OH
C5
O3P O CH2 H H OH
In second step, C1 notation changes from to (anomers specifying OH positioning on C1 with respect to C4 group) In step 2, PPi is hydrolyzed to 2Pi (irreversible, committing step)
Coupling of Reactions
Hydrolyzing a phosphate from ATP is relatively easy
G= -30.5 kJ/mol If endergonic reaction released energy into cell as heat energy, wouldnt be useful Must be coupled to an exergonic reaction
Note: You should be able to do this calculation for the synthesis of any of the nucleoside monophosphates
Rate of AMP production increases with increasing concentrations of GTP; rate of GMP production increases with increasing concentrations of ATP
Total amounts of purine nucleotides controlled Relative amounts of ATP, GTP controlled
Adenosine Degradation
Xanthosine Degradation
Ribose sugar gets recycled (Ribose-1-Phosphate R-5-P ) can be incorporated into PRPP (efficiency) Hypoxanthine is converted to Xanthine by Xanthine Oxidase Guanine is converted to Xanthine by Guanine Deaminase Xanthine gets converted to Uric Acid by Xanthine Oxidase
Xanthine Oxidase
A homodimeric protein Contains electron transfer proteins
FAD Mo-pterin complex in +4 or +6 state Two 2Fe-2S clusters
Purine Salvage
Adenine phosphoribosyl transferase (APRT)
Gout
Impaired excretion or overproduction of uric acid Uric acid crystals precipitate into joints (Gouty Arthritis), kidneys, ureters (stones) Lead impairs uric acid excretion lead poisoning from pewter drinking goblets
Xanthine oxidase inhibitors inhibit production of uric acid, and treat gout Allopurinol treatment hypoxanthine analog that binds to Xanthine Oxidase to decrease uric acid production
Choi HK, Atkinson K, Karlson EW et al. . 2004. Alcohol intake and risk of incident gout in men: a prospective study. Lancet 363: 1277-1281
Lesch-Nyhan Syndrome
Causes increased level of Hypoxanthine and Guanine ( in degradation to uric acid) stimulates production of purine nucleotides (and thereby increases their degradation)
Also,PRPP accumulates
Causes gout-like symptoms, but also neurological symptoms spasticity, aggressiveness, self-mutilation First neuropsychiatric abnormality that was attributed to a single enzyme
Purine Autism
25%
of autistic patients may overproduce purines To diagnose, must test urine over 24 hours
Biochemical findings from this test disappear in adolescence Must obtain urine specimen in infancy, but its difficult to do!
Pink urine due to uric acid crystals may be seen in diapers
IN von GIERKES DISEASE, OVERPRODUCTION OF URIC ACID OCCURS. THIS DISEASE IS CAUSED BY A DEFICIENCY OF GLUCOSE-6-PHOSPHATASE.
EXPLAIN THE BIOCHEMICAL EVENTS THAT LEAD TO INCREASED URIC ACID PRODUCTION? WHY DOES HYPOGLYCEMIA OCCUR IN THIS DISEASE? WHY IS THE LIVER ENLARGED?
Pyrimidine Synthesis
O
C HN CH C N COO
O3P O CH2 H H OH OH O H H
O
C
C HN CH C N H Orotate
Reduced Quinone
O
PRPP PPi
2-
NH2 O C O PO3-2
C O
COO
Orotidine-5'-monophosphate (OMP)
Carbamoyl Phosphate
Aspartate Aspartate Transcarbamoylase (ATCase)
Dihydroorotate Dehydrogenase
Pi
Quinone
O
HN
C CH CH N
C O
O3P O CH2 H H OH OH O H H
C
Dihydroorotase
Carbamoyl Aspartate
2 condensation rxns: form carbamoyl aspartate and dihydroorotate (intramolecular) Dihydroorotate dehydrogenase is an intramitochondrial enzyme; oxidizing power comes from quinone reduction Attachment of base to ribose ring is catalyzed by OPRT; PRPP provides ribose-5-P Channeling: enzymes 1, 2, and 3 on same chain; 5 and 6 on same chain
PPi splits off PRPP irreversible
FINAL REACTION OF PYRIMIDINE PATHWAY ANOTHER MECHANISM FOR DECARBOXYLATION A HIGH ENERGY CARBANION INTERMEDIATE NOT NEEDED NO COFACTORS NEEDED ! SOME OF THE BINDING ENERGY BETWEEN OMP AND THE ACTIVE SITE IS USED TO STABILIZE THE TRANSITION STATE
PREFERENTIAL TRANSITION STATE BINDING
Nucleoside monophosphate kinase catalyzes transfer of Pi to UMP to form UDP; nucleoside diphosphate kinase catalyzes transfer of Pi from ATP to UDP to form UTP CTP formed from UTP via CTP Synthetase driven by ATP hydrolysis Glutamine provides amide nitrogen for C4 in animals
*Purine synthesis inhibited by ADP and GDP at ribose phosphate pyrophosphokinase step, controlling level of PRPP also regulates pyrimidines
Orotic Aciduria
Caused by defect in protein chain with enzyme activities of last two steps of pyrimidine synthesis Increased excretion of orotic acid in urine Symptoms: retarded growth; severe anemia Only known inherited defect in this pathway (all others would be lethal to fetus) Treat with uridine/cytidine
IN-CLASS QUESTION: HOW DOES URIDINE AND CYTIDINE ADMINISTRATION WORK TO TREAT OROTIC ACIDURIA?
Degradation of Pyrimidines
Deoxyribonucleotide Formation
Biosynthetic pathways are only for ribonucleotide production Deoxyribonucleotides are synthesized from corresponding ribonucleotides
DNA composed of deoxyribonucleotides Ribose sugar in DNA lacks hydroxyl group at 2 Carbon Uracil doesnt (normally) appear in DNA
Thymine (5-methyluracil) appears instead
Formation of Deoxyribonucleotides
Reduction of 2 carbon done via a free radical mechanism catalyzed by Ribonucleotide Reductases
E. coli RNR reduces ribonucleoside diphosphates (NDPs) to deoxyribonucleoside diphosphates (dNDPs)
RIBONUCLEOTIDE REDUCTASE
R1 SUBUNIT
Three allosteric sites
R2 SUBUNIT
Tyr 122 radical Binuclear Fe(III) complex
During the overall process, a pair of SH groups provides the reducing equivalents
A protein disulfide group is formed Gets reduced by two other sulfhydryl gps of Cys residues in R1
Fes are bridged by O-2 and carboxyl gp of Glu 115 Tyr 122 is close to the Fe(III) complex stabilization of a tyrosyl free-radical
Chime Exercise
E. coli Ribonucleotide Reductase:
3R1R and 4R1R: R1 subunit 1RIB and 1AV8: R2 subunit Explore 1AV8: Ribonucleotide Reductase in detail.This is the R2 subunit of E. coli Ribonucleotide Reductase. The biological molecule consists of a heterotetramer of 2 R1 and two R2 chains. Identify the following structures:
8 long -helices in one unit of R2 Tyr 122 residue The binuclear Fe (III) complex The ligands of the Fe (III) complex
Free Radical Involvement of multiple SH groups RR is left with a disulfide group that must be reduced to return to the original enzyme
RIBONUCLEOTIDE REDUCTASE
dTTP
RIBONUCLEOTIDE REDUCTASE
CATALYTICALLY ACTIVE (R1)2 TETRAMER FORMATION (R1)4a (ACTIVE STATE) == (R1)4b (INACTIVE) CATALYTICALLY ACTIVE HEXAMERS (R1)6
Thioredoxin
Physiologic reducing agent of RNR Cys pair can swap H atoms with disulfide formed regenerate original enzyme
Thioredoxin gets oxidized to disulfide
Oxidized Thioredoxin gets reduced by NADPH ( final electron acceptor) mediated by thioredoxin reductase
Thymine Formation
Formed by methylating deoxyuridine monophosphate (dUMP) UTP is needed for RNA production, but dUTP not needed for DNA
If dUTP produced excessively, would cause substitution errors (dUTP for dTTP)
dUTP hydrolyzed by dUTPase (dUTP diphosphohydrolase) to dUMP methylated at C5 to form dTMP rephosphorylate to form dTTP
1DUD: Deoxyuridine-5'-Nucleotide Hydrolase in a complex with a bound substrate analog, Deoxyuridine-5'-Diphosphate (dUDP). Explore dUTPase as follows:
Find the substrate in its binding site Find C5 on the Uracil group. Is there enough room to attach a methyl group to C5? Locate the ribose 2 C. What protein group sterically prevents an OH group from being attached to the 2 C atom? Find the H-bond donors and acceptors (to the uracil base) from the protein. What would be the effect on the H-bonding if the base was changed to cytosine?
Tetrahydrofolate (THF)
Oxidized to dihydrofolate
Only known rxn where net oxidation state of THF changes THF Regeneration:
reductase)
thymidylate synthase
N5,N10 METHYLENE-THF
DHF
GLYCINE
serine hydroxymethyl transferase
NADPH + H+
dihydrofolate reductase
NADP+
THF
SERINE
thymidylate synthase
N5,N10 METHYLENE-THF
X
DHF
GLYCINE
serine hydroxymethyl transferase
FdUMP
NADPH + H+
dihydrofolate reductase
NADP+
X
SERINE
THF
Anti-Folate Drugs
(fluorodeoxyuridylate irreversible inhibitor) also affects rapidly growing normal cells (hair follicles, bone marrow, immune system, intestinal mucosa)
Adenosine Deaminase
CHIME Exercise: 2ADA Enzyme catalyzing deamination of Adenosine to Inosine / barrel domain structure TIM Barrel central barrel structure with 8 twisted parallel -strands connected by 8 -helical loops Active site is at bottom of funnel-shaped pocket formed by loops Found in all glycolytic enzymes Found in proteins that bind and transport metabolites
IN-CLASS QUESTION: EXPLAIN THE BIOCHEMISTRY THAT RESULTS WHEN A PERSON HAS ADA DEFICIENCY (HINT: LYMPHOID TISSUE IS VERY ACTIVE IN DEOXYADENOSINE PHOSPHORYLATION)
ADA DEFICIENCY
ONE OF FIRST DISEASES TO BE TREATED WITH GENE THERAPY ADA GENE INSERTED INTO LYMPHOCYTES; THEN LYMPHOCYTES RETURNED TO PATIENT PEG-ADA TREATMENTS
ACTIVITY LASTS 1-2 WEEKS