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Glossary of molecular biology: nucleic acids

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adenine

adenine
guanine

guanine
cytosine

cytosine
thymine

thymine
uracil

uracil
purine glycosidic bond
b/w N-9 of ring and 1'C of sugar
pyrimidine glycosidic bond
b/w N-1 of ring and 1'C of sugar
nucleases
cut phosphodiester bonds
exonucleases
remove terminal nucleotides only
endonucleases
cut b/w internal nucleotides
secondary structure of DNA, sometimes RNA
double helix

can form b/w any ANTIPARALLEL and COMPLEMENTARY sequences:
1) dsDNA
2) inverted complementary sequences within RNA
3) RNA + DNA
ds strands held together by
1) H bonds
2) base stacking
H bonds b/w base pairs
A-T/T-U: 2 H bonds
G-C: 3 H bonds (more stable)
base stacking
rings stacked over one another in interior of double helix

hydrophobic interactions add stability
intercalating agents
slide b/w neighboring base pairs in DNA

DNA can't be good template --> inhibits replication + transcription

ex: actinomycin D
replication
DNA to DNA
transcription
DNA to RNA
translation
RNA to proteins
denaturation
disrupts H bonds and hydrophobic but not covalent bonds

separates 2 strands
A-T rich sequences
usually found where DNA replication or RNA transcription initiates, since 2 strands must separate
NaOH + DNA
denatures 2/2 pH change

ionizes protons in H-N of base rings --> disrupts H bonds
temp + DNA
denatured over 80-90 deg C
chemicals + DNA
formamide + urea both denature DNA by interfering with H-bonds
most DNA structure
R-handed antiparallel helix
conformations of linear DNA
B DNA
Z DNA
A DNA
B DNA
most common
classic R-handed antiparallel helix with bases stacked on top of one another perpendicular to axis of helix

helix contains 2 grooves (major + minor) = where DNA-protein interactions occur

10.5 bp/turn
Z DNA
rare
found in sequences that are 1) G-C rich or 2) have long tracts of alternating purines & pyrimidines

L-handed antiparallel helix

occurs occasionally within B DNA chromosome
A DNA
anhydrous form of B DNA

R-handed antiparallel helix

bases not perfectly perpendicular to axis (20deg tilt)

found in RNA-DNA hybrids
circular DNA
found in mitochondrial DNA, most prok DNA, some viral DNA

can be relaxed or compacted by supercoils

no ends, therefore resistant to exonucleases
topoisomerases
relieve tension in supercoils of replicating DNA

make transient breaks (cut + reseal phosphodiester bonds) in DNA strands
deoxynucleotide synthesis inhibitors
used as antineoplastic agents
5-fluorouracil
inhibits thymidylate synthetase
hydroxyurea
inhibits ribonucleotide reductase
nucleotide degradation
phosphate group and pentose removed

amino groups attached to ring(s) removed as ammonia by adenosine deaminase + glutamine deaminase
purine degradation
purine ring can't open so just make it soluble as possible so it can be excreted
end product of purine degradation
uric acid
pyrimidine degradation
pyrimidine ring can be opened and partially degraded
thymidine degraded to
butyrate
uracil + cytosine degraded to
beta-alanine
purine/pyrimidine metabolism defects
esp. in purine degradation

1) Gout
2) Lesch-Nyhan syndrome
3) SCID
gout
excess uric acid production

precipitates in joints --> inflammation

kidney dz 2/2 accumulation of uric acid in tubules

mostly in men
elevated uric acid causes
gout
2ndary to disorder with high NA turnover (polycythemia, leukemia)
gout tx
allopurinol = xanthine oxidase inhibitor
xanthine oxidase
catalyzes sequential oxidation of hypoxanthine to xanthine to uric acid
lesch-nyhan syndrome
deficiency in enzyme hypoxanthine-guanine phosphoribosyl transferase (HGPRT)

results in inability to recycle purines + overproduction of uric acid
lesch-nyhan sx
MR
hyperuricemia
gout
compulsive self-destructive behaviors
ADA-deficient SCID
adenosine deaminase (purine salvage pathway) deficiency --> defective B + T cell development

dATP accumulates in RBCs, which allosterically inhibits ribonucleotide reductase (required for DNA synthesis

must live in sterile environment

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