DSA 1: Nucleic Acid structure and function

Question 1

allopurinol

Answer 1

purine analog used to treat gout (egress uric acid). Purines are carbolized to uric acid (low water solubility), but allopurinol is converted to alloxanthine (AX) by xanthine oxidase (XO). AX competitively inhibits XO, decreasing uric acid and increasing xanthine and hypoxanthine, the mixture of these 3 is more soluble.

Question 2

5-fluorodeoxyuracil

Answer 2

Structural analogs of purines, like 5-fluorodeoxyuracil are used as inhibitors of nucleotide biosynthesis through incorporation into DNA/RNA and are used in cancer treatments

Question 3

A-form DNA

Answer 3

Favored in solution without H2O, 11bp/RH turn, 26 Å in diameter, 2.6 Å rise/bp

Question 4

B-form DNA

Answer 4

10.5 bp/RH turn, 20 Å in diameter, and 3.4 Å rise/bp

Question 5

Z-form DNA

Answer 5

contain certain CG sequences or 5-methyl-C and G, 12.0bp/LH turn, 18 Å in diameter, and 3.7 Å rise/bp

Question 6

polymerase I/RNase H

Answer 6

Primers are removed by polymerase I in prokaryotes (has a bidirectional exonuclease activity) and by RNase H in eukaryotes (degrades RNA w/ 5’ to 3’ exonuclease) . The gaps are filled by polymerase δ and joined by ligase

Question 7

DNA polymerases

Answer 7

Different polymerases have different roles’ eukaryotes have α, δ, and ε polymerases (α is in complex with primase). In mammals δ does leading strand synthesis, primase/α complex does primers and beginning of Okazaki fragments, and ε does rest of fragments. In E. Coli, pol III does major synthesis besides primers done by primase, and pol I removes primers and fills gaps. Pol III, δ, and ε all have 3’ to 5’ exonuclease proofreading activity

Question 8

other replication proteins

Answer 8

Other proteins at fork are the clamp loading protein (replication protein C-RPC) which loads the sliding clamp (proliferating cell nuclear antigen-PCNA) which DNA polymerase binds to . As DNA replication starts, helicase (dnaB) unwinds the DNA which is held apart by single-stranded DNA binding proteins. Topoisomerase allows the strands to swivel upstream of the fork to eliminate stress. Gyrase (type II topoisomerase) is a target in antimicrobial and chemotherapeutics

Question 9

ciprofloxacin

Answer 9

Gyrase (type II topoisomerase) inhibitor in bacteria

Question 10

nalidixic acid

Answer 10

Gyrase (type II topoisomerase) inhibitor in bacteria

Question 11

etoposide

Answer 11

Gyrase (type II topoisomerase) inhibitor in humans

Question 12

doxorubicin

Answer 12

Gyrase (type II topoisomerase) inhibitor in humans

Question 13

autonomously replicated sequences (ARSs)

Answer 13

ASRs include 11bp sequences conserved in many other ASRs where the protein complex (origin recognition complex aka ORC) binds to the origin

Question 14

Rett Syndrome

Answer 14

severe neurological disease in females due to mutation in methyl-cytosine binding protein 2 (MeCP2), which represses transcription when bound to methyl cytosine in DNA. Begins at 1-2 years of age and leads to loss of motor and cognitive skills, seizures, autism, repetitive movements and death between 12 and 40 years.

Question 15

acetylation

Answer 15

acetylation of lysine destabilizes chromatin structures and favors transcription (looses + charge to interact with - DNA).

Question 16

Methylation

Answer 16

Methylation of some lys side chains of histones favors condensation into heterochromatin, but methylation of other lys and arg chains does the opposite. Also, about 3% of cytosine in humans is methylated; this is a heritable change that contributes to epigenetic inheritance. Methylation is also involved in gene regulation of CpG islands near gene promoters (~60% are methylated in humans), suppression of mobile elements by methylation of CG sequences near them, X chromosome inactivation (Barr body) by widespread methylation, and imprinting where some genes are methylated selectively depending on whether they’re from male or female germ line (related to gene silencing)

Question 17

cenH3 or CENP-A

Answer 17

At the centromere, H3 is replaced by centromeric H3 (cenH3) or CENP-A in all organisms; required for assembly of kinetochore proteins. When chromosomes replicate, nucleosomes are distributed to progeny strands, so CenH3 remains in centromeres of daughter strands (example of epigenetic inheritance)