NUCLEOTIDES LECTURE 1 Flashcards by Lamija Mrndic

what is the de novo pathway?

bacteria use this
synthesis of nucleotides from starting materials
highly conserved in eukaryotes

How well did you know this?

Not at all

Perfectly

what is the salvage pathway?

recovery of bases from food to make new nucleotides
more divergent, varied
most nucleotides come from this pathway

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

what does “base” mean?

the aromatic part

How well did you know this?

Not at all

Perfectly

what does “-side” mean?

no phosphate

How well did you know this?

Not at all

Perfectly

what does “‘tide” mean?

means phospho sugar (at different places on the sugar)
nucleotide=nucleoside phosphate

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

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

How well did you know this?

Not at all

Perfectly

what are the two types of riboses?

ribose and deoxyribose
different by the 2’OH being present on the ribonucleotide
deoxy=DNA
ribo=RNA

How well did you know this?

Not at all

Perfectly

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)

How well did you know this?

Not at all

Perfectly

what are the most common places for phosphate to be on the sugar?

3’ or 5’

How well did you know this?

Not at all

Perfectly

what is the stereochemistry of ribose sugars in the body

D sugars
furanose conformation

How well did you know this?

Not at all

Perfectly

what are the structures of the 5 bases, the names of the bases, the names of the nucleosides and the names of the nucleotides?

How well did you know this?

Not at all

Perfectly

what is the structure of adenine?

How well did you know this?

Not at all

Perfectly

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