Flashcards in Biochemistry Deck (293)
What gives DNA its (-) charge?
What gives histones their (+) charge?
Lysine and Arginine (what the octamer subunits primarily consist of)
What histones make up the nucleosome core in the "bead" on a string of chromatin? What histone ties the nucleosome "beads" together in a string?
Nucleosome core histones: H2A, H2B, H3, H4
H1 is the only histone that's not in the nucleosome core; it ties the nucleosome core/beads together in a "string"
*referring to chromatin here (chromatin is the condensed form of DNA that allows it to fit into the nucleus)
Heterochromatin vs Euchromatin
Heterochromatin: highly condensed, transcriptionally inactive, sterically inaccessible
Euchromatin: less condensed, transcriptionally active, sterically accessible
How to mismatch repair enzymes distinguish between old and new strands?
Because template strand cytosine and adenine are methylated in DNA replication; this allows mismatch repair enzymes distinguish between old and new strands
What does hypermethylation do to DNA transcription?
inactivates transcription of DNA ("methylation makes DNA mute")
What does histone acetylation do?
Relaxes DNA coiling, allowing for transcripiton ("acetylation makes DNA active")
List the Purines. How many rings?
PURe As Gold: Adenine and Guanine
Have 2 rings
List the Pyrimidines. How many rings?
CUT the PY: Cytosine, Uracil, Thymine
Have 1 ring
RNA vs DNA nucleotides?
Uracil in RNA
Thymine in DNA
Which nucleotide has a ketone?
Which has a methyl?
Which makes uracil when deaminated?
Guanine has a ketone
Thymine has a methyl
Deamination of cytosine makes uracil
G-C vs A-T bonds:
G-C --> have 3 H-bonds, stronger than A-T bonds, which have 2 H-bonds
the more G-C content, the higher the melting point
Nucleoside vs Nucleotide
Nucleoside = base + ribose (sugar)
Nucleotide = base + ribose + phosphate; linked by 3'-5' phosphodiester bond
Which amino acids are necessary for purine synthesis?
Convert ribonucleotides to deoxyribonucleotides in de novo pyrimidine synthesis (UDP --> dUDP)
1) Start with sugar + phosphate (PRPP)
2) Add base
1) Make temporary base (orotic acid)
2) Add sugar + phosphate (PRPP)
3) Modify base
Rate limiting enzyme in Purine synthesis?
Glutamine-PRPP-Amidotransferase (catalyzes step from PRPP --> --> --> IMP)
Rate limiting enzyme in Pyrimidine synthesis?
CPS - 2 = carbamoyl phosphate synthetase 2 (catalyzes step from ATP + CO2 + Glutamine --> Carbamoyl Phosphate)
anti-cancer drug; inhibits ribonucleotide reductase (UDP-->dUDP)
blocks de-novo purine synthesis by blocking PRPP synthetase (Ribose-5-P --> PRPP)
Inhibits thymidylate synthase (dUMP --> dTMP)
(get decreased dTMP)
inhibits dihydrofolate reductase (DHF-->THF); [thymidylate synthase uses THF (tetrahydrofolate), the active form of folic acid, to convert dUMP-->dTMP]
(get decreased dTMP)
inhibits bacterial dihydrofolate reductase (get decreased dTMP)
inhibits IMP (inosine monophosphate) dehydrogenase (IMP-->GMP)
How would a folic acid deficiency affect pyrimidine synthesis?
Thymidylate synthase (converts dUMP --> dTMP) uses THF, which is the active form of folic acid. So, without it, get decreased dTMP.
increased orotic acid in urine, megaloblastic anemia (that does not improve with vitamin B12 or folic acid), FTT; no hyperammonemia
Orotic aciduria (inability to convert orotic acid to UMP in the de novo pyrimidine synthesis pathway; d/t defect in either orotic acid phosphoribosyltransferase or orotidine-5'-phosphate decarboxylase)
-treat with oral uridine administration
What is the cause of orotic aciduria?
can't convert orotic acid to UMP in the de novo pyrimidine synthesis pathway; due to a defect in either orotic acid phosphoribosyltransferase or orotidine 5'-phosphate decarboxylase
Adenosine Deaminase Deficinecy
Results in SCID (severe combined immunodeficiency disease)
can't convert adenosine-->inosine in the purine salvage pathway, so get excess ATP and dATP, and thus feedback inhibition of ribonucleotide reductase (which imbalances the nucleotide pool); so prevents DNA synthesis and thus decreases the lymphocyte count