NUCLEOTIDES LECTURE 1 Flashcards
what is the de novo pathway?
bacteria use this
synthesis of nucleotides from starting materials
highly conserved in eukaryotes
what is the salvage pathway?
recovery of bases from food to make new nucleotides
more divergent, varied
most nucleotides come from this pathway
what are the starting materials of the purine pathway and what is the final goal?
starting materials: PRPP, glutamine, aspartate, CO2, glycine formate
the goal molecule is IMP (inosine monophosphate)
what are the starting materials of the pyrimidine pathway and what is the goal molecule?
starting materials: PRPP, glutamine, aspartate, CO2
goal: UMP (uridine monophosphate)
what does “base” mean?
the aromatic part
what does “-side” mean?
no phosphate
what does “‘tide” mean?
means phospho sugar (at different places on the sugar)
nucleotide=nucleoside phosphate
structure of a purine
2 fused rings
6+5 membered
nitrogens are on odd numbers except number 5 (1,3,7,9)
the link to ribose is on nitrogen 9
structure of a pyrimidine?
just one 6 membered ring
nitrons on 1 and 3 but not 5
the link to ribose is nitrogen number 1
what are the two types of riboses?
ribose and deoxyribose
different by the 2’OH being present on the ribonucleotide
deoxy=DNA
ribo=RNA
what is the bond between the sugar and the base?
beta glycosidic bond (points up)
the link to the base is on the 1’ carbon (use prime to know youre talking about ribose)
what are the most common places for phosphate to be on the sugar?
3’ or 5’
what is the stereochemistry of ribose sugars in the body
D sugars
furanose conformation
what are the structures of the 5 bases, the names of the bases, the names of the nucleosides and the names of the nucleotides?
what is the structure of adenine?
what is the structure of guanine?
what is the structure of cytosine?
what is the structure of uracil?
what is the structure of thymine?
what is the structure of hypoxanthine, the nucleoside and the nucleotide?
hypoxanthine is the step before you make A or G
nucleoside: inosine
nucleotide: IMP, inosinate
what is the structure of xanthine, the nucleoside and the nucleotide?
nucleoside: xanthosine
nucleotide: xanthylate, XMP
what is the structure of orotate (orotic acid), the nucleoside and the nucleotide?
nucleoside: orotidine
nucleotide: orotidylate, OMP
what is the structure of uric acid?
only base form in the degradation pathway
purine cube
pyrimidine cube
what is the structure of caffeine?
what is the structure of theobromine and where is it found?
found in chocolate
what is the structure of dideoxycytidine and what is it used for?
dideoxy=missing 2 oxygens
used as an antiviral
chain terminating reagent
terminates, can be used for DNA sequencing
what is the structure of AZT?
how are bases in RNA and DNA modified?
they are methylated
80ish modifications are known
tRNAs are heavily modified (up to 25% of the bases)
rRNAs have methylated bases
what are some specific base methylations?
1-2% in animals and 5-8% in plants of DNA bases are 5-Me-Cytosine
1-2% of DNA bases in E.coli are 6-Me-Adenine
some bases are also glycosylated
where do the atoms on a purine come from in the de novo pathway?
what are the steps of de novo synthesis of purines?
purine ring assembled on ribose phosphate
step 1: 5-phosphoribose -> PRPP (ATP->AMP)
step 2: PRPP-> 5-phosphoribosylamine (take two phosphates off and add amine)
11 steps to make IMP
7 high energy phosphate bonds
where does regulation happen in the de novo synthesis of purines?
regulation at steps 1 and 2
pathway is committed at step 2
PRPP can be used for other things
characteristics of PRPP
phosphoribosyl pyrophosphate
key intermediate in nucleic acid and AA synthesis
complex regulation
alpha sugar anomer, inversion at the step after
characteristics of phosphoribosylamine
committing step, purine specific regulation
anomeric inversion to make the beta anomer
making this compound releases PPi, which is irreversible
as soon as PPi is released it is hydrolysed, irreversible
glutamine N donor
what are some nitrogen donors?
glutamine (N carrier) turns into glutamate
nitrogen is taken from the side chain
aspartate turns into fumarate
nitrogen is taken from the backbone
how is an aldehyde (ketone) made into an amine?
phosphoester intermediate
phosphate from ATP or GTP
N from glutamine side chain or aspartic acid backbone
