Nucleotides Flashcards
3 subunits of nucleotides
- pentose sugar (ribose in RNA or deoxyribose in DNA)
- nitrogenous base (purines or pyramidines)
- phosphate group which forms the linkage between nucleotides)
what is a nucleoside
a nitrogenous base + a pentose sugar (ribose or deoxyribose)
nucleotides are linked by what bond?
3’-5’ phosphodiester bond
by convention, DNA sequences are written from the ___ —> ___ end
5’ —-> 3’ end
the difference in the sugar group between RNA and DNA
the pentose sugar in DNA lacks a hydroxyl (OH) grp at the 2’ Carbon
What are the 3 purines that aren’t used in DNA?
- xanthine
- hypoxanthine
- uric acid
how many rings are in purines? in pyramydines?
Purines: 2– PURe As Gold– you always want more rings of gold
PYramidines: 1- you should try to have only 1 slice of PY
Uracil is found only in… Thymine is found only in…
Uracil: RNA
Thymine: DNA
can the pyramidines be derived from one another and if so, how?
yes:
- deaminating cytosine gives you a uracil
- adding a methyl group to uracil gives a thymine
What are effective carriers? What are the effective carriers of: ATP: NADH/NADPH, FADH2: UDP glucose: SAM: THF: biotin: Coenzyme A:
Effective carriers are molecules that are relatively stable as leaving groups. The effective carriers of: ATP: phosphoryl NADH/NADPH, FADH2: electrons UDP glucose: sugars SAM: methyl THF (tetrahydrofolate): 1 carbon biotin:CO2 Coenzyme A: acyl
What is a transition mutation?
a mutation that substitutes a purine for another purine, or a pyrimidine for another pyrimidine
What is a transversion mutation?
a mutation that substitutes a pyrimidine for a purine or vice versa
The more C-G bonds in a DNA chain the __________
higher the melting point (temp needed to denature it) because C-G has three H-bonds as opposed to two in A-T
This is important for PCR/other experiments where you have to denature DNA
What is Chargaff’s rule?
in DNA, the %A = the %T and the %C = %G
Is DNA positively or negatively charged? What about histones?
DNA: negatively (an acid, leaves an H+, has a negative charge)
Histones: positively
what is the structure of a nucleosome bead?
2 loopes of negatively charged DNA wrapped around 8 positively charged histones (H2a, H2b, H3,H4- each x2)
histones are rich in which two aa?
lysine and arginine
which histones form the octamer in the nucleosome bead? which histone ties nucleosome beads together in a string (and is the only histone that is NOT part of the nucleosome core)?
octamer: H2a, H2b, H3, H4 (each x2)
ties nucleosomes together: H1
in mitosis, DNA condenses to form…
chromosomes
Heterochromatin
HeteroChromatin = Highly Condensed DNA
-transcriptionally inactive, sterically inaccessible
Euchromatin
Euchromatin = Expressed
- less condensed, transcriptionally active, sterically accessible DNA
which nucleotides in the template strand are methylated during DNA replication and why?
cytosine and adenine are methylated in DNA replication because it allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes (VERIFY THAT THIS ONLY HAPPENS IN PROKARYOTES– FIRST AID, p.64)
Hisone methylation does what to DNA? What about histone acetylation?
histone Methylation = Mute DNA (inactivates transcription)
Acetylation = Active DNA (relaxes DNA coiling, allowing for transcription)
What are the Purines used in DNA/RNA?
Adenine
Guanine
“PURe As Gold”
What are the Pyramidines used in DNA? In RNA?
DNA: Cytosine, Thymine
RNA: Cytosine, Uracil
“CUT the PY” (pyramindines = cytosine, uracil, thymine)
What is the defining feature of Guanine?
2 ring nucleotide with a ketone
What is the defining feature of Thymine?
1 ring nucleotide with a methyl
THYmine = meTHYl
the deamination of cytosine (a 1 ring nucleotide) makes…
uracil
how many H-bonds are in C-G pairs? A-T pairs? And what does this mean?
C-G: 3 H bonds
A-T: 2 H bonds
*DNA strands with more C-G pairs have a higher “melting point” for denaturing
what 4 cofactors are necessary for de novo purine synthesis?
- THF- Tetrahydrafolate + GAG (3 aa)
- Glycine
- Aspartate
- Glutamine
2 pathways for purine synthesis, and what they are most commonly used for
- de novo synthesis: rapidly dividing cells
2. salvage synthesis: major route for synthesis in adults
de novo purine synthesis
uses elemental precursors and is used for rapidly dividing cells
salvage purine synthesis
recycles 90% of preformed purines released when cells’ nucleases degrade endogenous DNA/RNA to make new purine nucleotides– it is the major route for synthesis in adults
the rate limiting step in de novo purine synthesis is made by
glutamine PRPP (5-phosphoribosyl-1-pyrophosphate) amidotransferase
PRPP amidotransferase, the enzyme in the rate limiting step of purine de novo synthesis, is inhibited by… (5)
downstream products: 1. inosine monophosphate (IMP) 2. guanosine monophosphate (GMP) 3. adenosine monophosphate (AMP) purine analogs 4. Allopurinol 5. 6-mercaptopurine
what is the reciprocal substrate effect in purine synthesis and what does it allow for?
GTP and ATP are substrates in AMP and GMP synthesis respectively, so if there’s less GTP —-> there’s less AMP and therefore —> less ATP. This allows for balanced synthesis of adenine and guanine nucleotides
a pyrimidine nucleotide always base pairs with ______
a purine nucleotide, and vice versa
what are the two purine analogs that inhibit PRPP amidotransferase (the rate limiting enzyme in de novo purine synthesis)
- Allopurinol
2. 6-mercaptopurine
salvage purine synthesis is catalyzed by which enzyme?
HGPRT (hypoxanthine-guanine phosphoribosyltransferase)
which converts hypoxanthine —> IMP and guanine —-> GMP
HGPRT (hypoxanthine-guanine phosphoribosyltransferase), the enzyme that catalyzes salvage purine synthesis, is inhibited by what (2)?
IMP and GMP (the products of the rxn)
- HGPRT converts hypoxanthine —> IMP and guanine —-> GMP
what is the fundamental rxn of salvage purine synthesis
nitrogenous base (guanine or hypoxanthine) + PRPP —–> GMP/IMP + PPi
what is Lesch-Nyhan Syndrome
Lesch-Nyhan Syndrome = Lacks purine Nucleotide Synthesis
-an x-linked recessive disorder of failed purine salvage due to the absence of HGPRT that leads to excess puirne synthesis/excess uric acid production (from the breakdown of otherwise salvageable guanine and hypoxanthine)
what is an x-linked recessive disorder of failed purine salvage due to the absence of HGPRT that leads to excess puirne synthesis/excess uric acid production (from the breakdown of otherwise salvageable guanine and hypoxanthine)
Lesch-Nyhan Syndrome (Lacks purine Nucleotide Synthesis)
how does Lesch Nyhan Syndrome (the absence of HGPRT– Lacks purine Nucleotide Salvage synth) present?
retardation cerebral palsy self-mutilation aggression gout choreoathetosis (involuntary movements) arthritis **nephropathy-- often the cause of death
how is Lesch Nyhan Syndrome (the absence of HGPRT– Lacks purine Nucleotide Salvage synth) diagnosed?
orange crystals in diaper, difficulty with movement, self-injury, hyperuricemia (high uric acid in the blood)
what is the prognosis for people with Lesch-Nyhan Syndrome (Lacks purine Nucleotide Salvage synthesis)
urate nephropathy, death in the first decade, usually as a result of renal failure
how does Lesch Nyhan Syndrome give you arthritis
uric acid is less soluble than hypoxanthine and xanthine —-> crystals deposit in joints and sot tissues —> arthritis
what is the treatment for Lesch Nyhan Syndrome (the absence of HGPRT– Lacks purine Nucleotide Salvage synth)
Allopurinol (purine analogue) which inhibits xanthine oxidase (so hypoxanthine, can’t be converted into xanthine, and xanthine can’t be converted into uric acid —> less crystalization!)
*** TXT DOES NOT AMELIORATE NEUROLOGIC SYMPTOMS
3 disorders associated with purine salvage deficiencies
- Lesch Nyhan Syndrome (the absence of HGPRT– Lacks purine Nucleotide Salvage synth)
- Gout (primary and secondary)
- Severe Combined (T and B) Immunodeficiency (SCID)
what is Gout?
a disorder in which overproduction or under excretion of uric acid —> hyperuricemia —> sodium urate crystals deposit in joints/soft tissue —> arthritis
primary gout
gout due to hyperuricemia without evident cause
- mt be familial
- PRPP synthetase hyperactivity
- HGPRT deficiency (Lesch Nyhan Syndrome)
secondary gout
aka acquired gout– when uric acid overproduction is caused by leukemia, myeloproliferative syndrom, multiple myeloma, hemolysis, neoplasia, psoriasis and alcoholism
or under excretion caused by kidney disease and drugs such aspirin, diuretics and alcohol
presentation of gout
monoarticular arthritis of distal joints (ie podagra- gout of the great toe)
- long H/O hyperuricemia (20-30yrs)
- nodular tophi (urate crystals surrounded by fibrous CT) around the joints/achilles tendon
what’s podagra?
gout of the great toe
what’s tophi?
urate crystals surrounded by fibrous CT– often seen in gout as nodules around the joints/achilles tendon
how is primary/secondary gout diagnosed?
- arthritis
- hyperuricemia
- detection of negatively birefringent crystals from articular tap
negatively birefringent crystals, characteristic of gout, are what color when parallel to polarized light? what color when perpendicular?
paraLLel = yeLLow perpendicuLar = bLue
positively birefringent crystals are characteristically found in…
pseudogout
what is the differential diagnosis for increased uric acid and gout
- Lesch-Nyhan
- Alcoholism
- other: G6P deficiency, hereditary fructose intolerance, galactose 1P uridyl transferase deficiency, all disorderswith increased accumulation of phosphorylated sugars, increased degradation products (eg AMP)
what is the treatment for primary or secondary gout (3)
- normalize the uric acid levels (allopurinol, probenecid for chronic gout)
- decrease pain/inflammation (colchicines, NSAIDS for acute gout)
- avoid large meals and EtOH
what is SCID?
severe combined (T &B) immunodeficiency: autosomal recessive disorder caused by deficiency in ADENOSINE DEAMINASE (ADA). This leads to an excess is ATP and dATP —>inhibits ribonucleotide reductase (catalyzes ribose —> deoxyribose) —-> imbalance in nucleotide pool —–> devastates lymphocytes
SCID (severe combined (T &B) immunodeficiency) is an autosomal reessive disorder caused by a deficiency in which enzyme?
Adenosine Deaminase (ADA)
- This leads to an excess is ATP and dATP —>inhibits ribonucleotide reductase (catalyzes ribose —> deoxyribose) —-> imbalance in nucleotide pool —–> devastates lymphocytes
how does SCID (severe combined (T &B) immunodeficiency) present?
children recurrently infected with bacterial, protozoan, and viral pathogens especially CANDIDA AND PNEUMOCYSTIS JIROVECI
children with SCID (severe combined (T &B) immunodeficiency) are frequently infected by which two pathogens that rarely affect people who are not immunocompromised?
Candida and Pneumocystis jiroveci
how is SCID (severe combined (T &B) immunodeficiency) diagnosed?
no plasma cells or B or T lymphocytes on CBC. No thymus
what is the treatment for SCID (severe combined (T &B) immunodeficiency)?
gene therapy, bone marrow transplantation
what is the prognosis for SCID (severe combined (T &B) immunodeficiency)
poor
like purines, pyrimidines are synthesized via what two pathways?
de novo and salvage synthesis
the pyrimidine salvage pathway relies on which enzyme?
pyrimidine phosphoribosyl transferase
the salvage pathway is responsible for for recycling what 3 things?
- orotic acid
- uracil
- thymine
IT IS NOT RESPONSIBLE FOR RECYCLING CYTOSINE
what is hereditary Orotic Aciduria?
Inability to convert orotic acid to UMP (de novo pyrimidine synthesis pathway) because of a defect in UMP synthase ( a bifunctional emzyme) (also known as orotate phosphoribosyl transferase and/or OMP decarboxylase (Orotidine 5’-phosphate)) —–> excessive excretion of orotic acid in urine.
deficiencies in orotate phosphoribosyl transferase and/or OMP decarboxylase and/or UMP synthase lead to what disorder?
hereditary Orotic aciduria: autosomal recessive
how does hereditary Orotic aciduria present?
retarded growth (failure to thrive) and severe anemia (doesn’t improve with B12 or folic acid)
how is hereditary Orotic aciduria diagnosed? (5)
- low serum iron
- leukopenia
- megablastic anemia (doesn’t improve with B12 or folic acid)
- white precipitate in the urine
- no hyperammoniemia (vs OTC deficiency (a urea cycle disorder))
how is hereditary Orotic aciduria treated?
synthetic cytidine or uridine is given to maintain pyrimidine nucleotide levels for DNA and RNA synthesis
what is a disease associated with problems with pyrimidine synthesis
Hereditary Orotic Aciduria– caused by a deficiency is orotate phosphoribosyl transferase and/or OMP decarboxylase
what is one of the products of purine degradation that is excreted in the urine?
uric acid
pyrimidine degradation yields what 3 things?
CO2
NH4+
B-amino acids
what is usually used as an indicator of DNA turnover in chemotherapy/radiation therapy and why?
B-aminoisobutyrate levels because thymine degradation is the only source of B-aminoisobutyrate (remember that pyrimidines are degraded into CO2, NH4+ and B-amino acids)
hydroxyurea is a chemotherapeutic agent that blocks which enzyme?
ribonucleotide reductase– the enzyme used to convert UDP to dUDP in the pyrimidine de novo synthesis pathway
5-flourouracil (5-FU) is a chemotherapeutic agent that inihibits which enzyme?
thymidylate synthase- which converts dUMP —> dTMP (decreases dTMP) in the pyrimidine de novo synthesis pathway
methotrexate (MTX) and pyrimethamine are chemotherapeutic agents which inhibit which enzyme?
dihydrofolate reductase- which leads to a reduction in dTMP in the pyrimidine de novo synthesis pathway
how can you distinguish between orotic aciduria caused by problems with pyrimidine synthesis and increased orotic acid seen in OTC deficiencies, a disorder of the urea cycle?
in hereditary orotic aciduria there is an increase in orotic acid, but no hyperammonemia, whereas in OTC deficiencies you see increased orotic acid with hyperammonemia
two steps in de novo purine synthesis
- Start with sugar (ribose 5-P) + phosphate (PRPP- Phosphoribosyl pyrophosphate)
- Add a base (—-> IMP —-> AMP or GMP)
5 Steps for pyrimidine de novo synthesis
- Make a temporary base (orotic acid)
- Add sugar (ribose 5-P) + phosphate (PRPP- Phosphoribosyl pyrophosphate)
- modify the base
- make ribonucleotides
- ribonucleotide reductase is used to convert ribonucleotides to deoxyribonucleotides
what is the temporary base used in pyrimidine synthesis
orotic acid
carbamoyl phosphate is a substrate in what two metabolic pathways
- de novo pyrimidine synthesis (carbamoyl phosphate —> orotic acid)
- the urea cycle
what is Ornithine transcarbamoylase (OTC) is an enzyme in what pathway, and what does an OTC deficiency lead to?
OTC is a key enzyme in the urea cycle
- a deficiency leads to a build up of carbamoyl phosphate, which instead of entering the urea cycle (bc it’s backed up from the enz. deficiency) enters pyrimidine de novo synthesis —-> converted to orotic acid —-> increased orotic acid + hyperammonemia)
Trimethoprim (TMP) is an antimetabolite (antibiotic) that inhibits…
bacterial dihidrofolate reductase (ie decreased dTMP (pyrimidine de novo synthesis) in bacteria
Adenosine Deaminase Deficiency leads to
SCID (severe combined immunodeficiency) via:
excess ATP and dATP —> imbalance in nucleotide pool via feedback inhibition of ribonucleotide reductase —> prevents DNA synthesis and thus decreases lymphocyte count
what was the first disease to be treated by experimental human gene therapy?
SCID
who is affected by SCID?
kids
what are the genetics behind ADA (adenosine deaminase) deficiency (which leads to SCID)?
autosomal recessive
what are the genetics behind HGPRT deficiency (which leads to Lesch Nyhan Syndrome
x-linked recessive
