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Flashcards in Biochemistry Deck (293)
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1

What gives DNA its (-) charge?

Phosphate groups

2

What gives histones their (+) charge?

Lysine and Arginine (what the octamer subunits primarily consist of)

3

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)

4

Heterochromatin vs Euchromatin

Heterochromatin: highly condensed, transcriptionally inactive, sterically inaccessible

Euchromatin: less condensed, transcriptionally active, sterically accessible

5

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

6

What does hypermethylation do to DNA transcription?

inactivates transcription of DNA ("methylation makes DNA mute")

7

What does histone acetylation do?

Relaxes DNA coiling, allowing for transcripiton ("acetylation makes DNA active")

8

List the Purines. How many rings?

PURe As Gold: Adenine and Guanine
Have 2 rings

9

List the Pyrimidines. How many rings?

CUT the PY: Cytosine, Uracil, Thymine
Have 1 ring

10

RNA vs DNA nucleotides?

Uracil in RNA
Thymine in DNA

11

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

12

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

13

Nucleoside vs Nucleotide

Nucleoside = base + ribose (sugar)
Nucleotide = base + ribose + phosphate; linked by 3'-5' phosphodiester bond

14

Which amino acids are necessary for purine synthesis?

Glycine
Aspartate
Glutamine

15

Ribonucleotide Reductase

Convert ribonucleotides to deoxyribonucleotides in de novo pyrimidine synthesis (UDP --> dUDP)

16

Purine synthesis

1) Start with sugar + phosphate (PRPP)
2) Add base

17

Pyrimidine synthesis

1) Make temporary base (orotic acid)
2) Add sugar + phosphate (PRPP)
3) Modify base

18

Rate limiting enzyme in Purine synthesis?

Glutamine-PRPP-Amidotransferase (catalyzes step from PRPP --> --> --> IMP)

19

Rate limiting enzyme in Pyrimidine synthesis?

CPS - 2 = carbamoyl phosphate synthetase 2 (catalyzes step from ATP + CO2 + Glutamine --> Carbamoyl Phosphate)

20

Hydroxyurea mechanism

anti-cancer drug; inhibits ribonucleotide reductase (UDP-->dUDP)

21

6-mercaptopurine mechanism

blocks de-novo purine synthesis by blocking PRPP synthetase (Ribose-5-P --> PRPP)

22

5-Fluorouracil mechanism

Inhibits thymidylate synthase (dUMP --> dTMP)
(get decreased dTMP)

23

Methotrexate mechanism

inhibits dihydrofolate reductase (DHF-->THF); [thymidylate synthase uses THF (tetrahydrofolate), the active form of folic acid, to convert dUMP-->dTMP]
(get decreased dTMP)

24

Trimethoprim mechanism

inhibits bacterial dihydrofolate reductase (get decreased dTMP)

25

Mycophenylate mechanism

inhibits IMP (inosine monophosphate) dehydrogenase (IMP-->GMP)

26

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.

27

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)
-Autosomal recessive
-treat with oral uridine administration

28

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
-Autosomal recessive

29

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

30

Absence of HGPRT

Lesch-Nyhan syndrome
-HGPRT converts hypoxanthine to IMP and guanine to GMP; without it, have defective purine salvage. Get excess uric acid production and de novo purine synthesis (so increased PRPP amidotransferase activity)
-X-linked recessive
-Findings: retardation, self-mutilation (lip-biting), aggression, hyperuricemia, gout, choreoathetosis
-Trtmnt: allopurinol (can't treat CNS symptoms)