Exam Flashcards
central dogma
replication, transcription, translation - DNA, RNA, protein
AT bonds
2
GC bonds
3 bonds
ten base pairs
0.34nm between stacked bases, 3.4nm per helical turns
semi conservative replication
each strand is template for new strand, new DNA has 1 parental and one new strand
conservative model
whole strand is conserved, whole new strand is made
dispersive model
bits of old and new in both
theta replication
most circular DNA like bacteria, bi and unidirectional, produces 2 circular molecules, does not break nucleotide strand
rolling circle replication
F factor of E.coli and some viruses, unidirectional, breaks nucleotide strand, produces 1 circular molecule and 1 linear molecule that may circularize
linear chromosome replication
eukaryotic, bidirectional, does not break strand, many replicons, produces 2 linear molecules
DNA replication requirements
DNA polymerase, 4dNTPs, single stranded template, RNA primer
DNA replication features
synthesized 5’-3’, strands held together by H bonds between bases
leading strand
add nucleotides 3’-5’ continuously, same direction as unwinding towards helicase
lagging strand
adds nucleotides 5’-3’ discontinuously, Okazaki fragments, opposite direction
okazaki fragments
1-2kb in prokaryotes, 0.1-0.2kb in eukaryotes
oriC
DNA replication origin in E.coli, AT bond rich, requires less energy to break
proteins in prokaryotic DNA replication
initiator proteins, DNA helicase, SSBP, DNA gyrase
DNA helicase
binds to replication fork and unwinds 5’-3’, breaks H bonds, travels on lagging strand ahead of replication machinery
single stranded binding protein (SSBP)
binds to unwound stands and prevent parent strands from annealing (hairpins), protects from nucleases
nucleases
want to break phosphodiester bonds
DNA gyrase
topoisomerase that makes double stranded breaks in DNA to relieve torsional strain, moves ahead of DNA helicase, Type 1-2
replication initiation prokaryotic
- initiator proteins bind to oriC and opens up to DNA
- DNA helicase binds to lagging strand to unwind DNA
- SSBP bind to unwound strands to keep DNA apart
- DNA gyrase binds upstream to replication fork
primase/RNA polymerase
synthesizes short RNA primer (~10) that provides 3’ OH end for DNA polymerase to begin synthesis
replication elongation prokaryotic
- 5’-3’ direction
- leading strand continuously synthesized by DNA polymerase III
- lagging strand synthesized in fragments
DNA polymerase III
elongates 5’-3’, requires recognition of RNA polymerase, 3’-5’ exonuclease, can back up to correct mistakes
DNA polymerase I
removes and replaces primers, 5’-3’ exonuclease activity to remove RNA primer
DNA ligase
joins Okazaki fragments together through phosphodiester bonds between 5’-phosphate group and 3’-OH group
lagging strand process
- when DNA pol.III reached 5’ end of RNA primer, pol.III swapped for pol.I
- pol.I removes RNA primer and re-synthesizes short tract of DNA
- DNA ligase makes phosphodiester bond between 5’-3’ group to become continuous
replication termination prokaryotic
occurs when helicase/replication forks meet, stops unwinding
unique aspects of eukaryotic chromosome replication
replication begins at AT rich replicating sequences, DNA helicase binds to initiator protein of double strands, shorter RNA primers/okazaki fragments
DNA polymerase alpha
generates RNA primer
DNA polymerase epsilon
performs leading strand replication
DNA polymerase delta
performs lagging strand replication
origin licensing
origins prepared for replication of G1 phase, begins in S phase, can replicate genome only once
basic features of RNA
ribose sugar and unstable 2’OH group, single stranded, many structure types for different functions
non-coding RNA/small ncRNA
small nucleolar RNA (snoRNA), small interfering RNA (siRNA), small nuclear RNA (snRNA)
