Chap 2 Flashcards
Nucleoside
Base, sugar, but no phosphate
RNA 2’ carbon
OH
Length of RNA is measured by
Nucleotide number
two strands/secondary structure is stabilized by
Base pairs h bonding (of backbone) and base stacking
Base stacking
Bases stack like stairs to keep together, keeps water out (hydrophobic)
Major groves
Wide grove- where proteins can interact with DNA the most
Minor grove
Narrower grove, interacted with less
B form/ watson crick form
Standard, right handed, 10.5 bp/turn, high humidity, low salt, 5’ to 3’, major groove is deep and minor grove is shallow and broad
A form
Right handed, 11bp/turn, low humidity, high salt, associated with RNA, major and minor grove is moderate,
Z DNA
Left handed, “single grove”, 12 bp/turn, high MgCl or ethanol and methylated cytosine, linked to certain diseases, can occur in vivo
Nucleic acid
polymers made up of nucleotides
Nucleotide
Nucleic acid subunits made of a sugar, phosphate, and nitrogenous base
Deoxyribose
H on 2’ C
Chargaffs rules
GC content varies across species, but within the species, it is the same
DNA is held together by
Covalent bonds (phosphodiester bonds) and h bonds (bases bonds)
Hyperchromicity
As dna melts, its absorption of UV increases
Melting temperature
The temp at which half the bases in the dsDNA sample has melted
Hybridization
Complementary base pairs from two different sources
Denaturation temp effected by
GC content, salt concentration (higher salt, higher temp), ph,
Reanneling rate effected by
Concentration of DNA, repeativity,
Cop curve ?
Show how long dna will reanneal
Slipped structure
(DNA 2nd) in short tandem repeats, can result in deletions and insertions
Cruciforms
At palindromes or inverted repeats, a loop is forms, leads to genetic instability,
Triple helices
(DNA 2nd) Happens in mirror repeats, extra strand pops up in major grove, leaves one DNA single stranded,
Hoogsteen base pairs
3 base pairs bonding, associated with friedreich ataxia (loss of muscular coordination and heart enlargement), alt ways to Watson crick bond
G quadruplex
(DNA2) 4 stranded in a stretch of tandem guanine, for gene regulation, found in telomeres and promoters
Super coiling is done to
Conserve space, put energy into DNA molecule (negative), unwinds DNA for replication, transcription and recombination (negative)
Linking number
Number of times two hydrogen bonded strands cross each other
Writhes
Number of time DNA helix is coiled about itself
Linking number formula
Twist plus writhes
Partial denaturation
Done to relieve strained supercoiling
Why does positive supercoiling occur
DNA replication and transcription (ahead of fork),
Topoisomerases
Release supercoiling
primary structure of DNA
nucleic acid and nucleotides, held by phosodiester bonds
fidelity of DNA replication
proofreading DNA repair mechanisms and correct mistakes
dsDNA has a - core
hydrophobic
negative supercoiling
saves space, energy into DNA molecule, almost all DNA in pro and euk is negatively supercoiled, under wound
DNA tertiary structure
supercoiling
RNP
Catalyze replication, transcription,
ribosome, the enzyme telomerase, vault ribonucleoproteins, RNase
