Lecture 6 - The Central Dogma Flashcards
the central dogma:
DNA is ___ into mRNA by ____ ___ ____
amino acids are placed on _____ by ____ ____ ____
the ribosome pairs ____ in ____ with ____ on ____ according to the ___ ____, ___ mRNA into ____
transcribed into mRNA by mRNA polymerase enzyme
tRNA by tRNA synthetase enzymes
codons in mRNA with anti-codons on tRNA according to the genetic code, translating mRNA into proteins
replication forks: bidirectional and discontinuous:
DNA is replicated ____ away from the ____
there is a unique ___ ___ site in E. coli, multiple ____ in higher eukaryotes
since both strands are synthesized from ___ to ___, the ____ strand must be synthesized in pieces (____ ____)
bidirectionally away from the origin
promoter region site in E. coli, multiple sites in higher eukaryotes
5’ to 3’, the lagging strand must be synthesized in pieces (okazaki fragments)
Polymerase mechanism review:
incoming dNTP is attacked at the ____ ____ by the ___ ___ of the growing DNA strand
Mg2+ ions help to ___ the ____ ___ ____
alpha phosphate by the 3’ hydroxyl of the growing DNA chain
pentavalent transition state
proofreading: exonuclease activity:
DNA polymerase proofreads newly synthesized DNA using its ___ to ___ ____ activity to remove errors, improving replication accuracy
3’ to 5’ exonuclease activity to remove errors, improving replication accuracy
proofreading: exonuclease activity:
- error detection
if an incorrect nucleotide is incorporated, the __ ___ end of the growing DNA strand becomes ____, blocking further ____
the DNA polymerase ___ __ in order to position the mispaired base in the ___ -> ___ exonuclease __ site
3’ -OH end of the growing DNA strand becomes misaligned, blocking further elongation
slides back in order to position the mispaired base in the 3’ -> 5’ exonuclease active site
proofreading: exonuclease activity:
- error removal
the incorrect nucleotide is ____ and ____ by the ___ ____
hydrolyzed and removed by the exonuclease domain
proofreading: exonuclease activity:
- resumption of synthesis
DNA polymerase slides ____ and resumes its ____ ____
forward and resumes its polymerization activity
proofreading: exonuclease activity:
DNA polymerase I contains:
DNA polymerase ___ ____
___ -> __ (___) exonuclease ___ ___
active site
3’ -> 5’ (proofreading) exonuclease active site
proofreading: exonuclease activity:
error rate is 1 in 10^___ with 3’ -> 5’ exonuclease activity (removal of nucleotides from the end of the DNA strand)
1 in 10^__ without exonuclease domain
10^8
10^5
replication initiation in bacteria:
- origin binding at DnaA-ATP
___ (origin of replication) is the specific site where bacterial replication begins
it contains ___ (___ ___ ___), a region rich in ___ base pairs, which are easier to ____ due to fewer ___ ___
DnaA (an ____ protein) binds to ___ using ___ –> this creates ____ ____ ____, which forces the ___ region to ___
oriC
DUE (DNA unwinding element), a region rich in AT base pairs, which are easier to separate due to fewer hydrogen bonds
(an initiator protein) binds to oriC using ATP –> this creates positive supercoiling, which forces the DUE region to unwind
replication initiation in bacteria:
- loading of DnaB Helicase by DnaC
DnaC (___ ___) helps recruit ___ ____
DnaB is loaded onto the ___-____ DNA and begins ___ the DNA helix
DnaC ____ ___ in order to release ___ and ____, completing the ___-___ process
(helicase loader) helps recruit DnaB helicase
single-stranded DNA and beings unzipping the DNA helix
hydrolyzes ATP in order to release DnaB and itself, completing the helicase-loading process
replication initiation in bacteria:
Dna-A uses the energy from ___ ___ to introduce a ___ ___ ___
this causes ___ that ___ the ___ ___ __ (___), which is just the ____-rich sequence at the ___ of ____
DnaC “___ ____” opens the ____ ____ ring and ____ it onto the ____
ATP hydrolysis to introduce a local positive supercoil
strain that unwinds the DNA unwinding element (DUE), which is just the AT-rich sequence at the origin of replication
“helicase loader” opens the DnaB helicase ring and loads it onto the ssDNA
DNA polymerase III
DNA polymerase I primarily fulfills a ____ ____, including removing ___ ____
most replication is carried out by ___ ___ ___, a ___ subunit complex
before DNA can be replicated, it must be ____ by ____ and separated by ____
the DNA polymerase III complex simultaneously synthesizes both ___ and ___ strands
repair function, including removing RNA primers
DNA polymerase III, a 10 subunit complex
unwound by topoisomerase and separated by helicase
leading and lagging strands
strand separation and primer synthesis:
both leading and lagging strand synthesis beging with ___ ___ (__-___ nt) which are synthesized by ____
DNA polymerase cannot create new strands from scratch, it requires a (___) ____
RNA primers (10-60 nt) which are synthesized by primase
(RNA) primer
clamp-loading complex:
___ binding induces a ___ ____ in the clamp-loading complex that opens the ___-____ ring for ___ insertion
the B-clamp (aka “___ ___”) inner surface is optimized for ___ interaction with DNA
the B-clamp tethers ___ ___ to ___, increasing processivity of pol III
ATP binding induces a conformational change in the clamp-loading complex that opens the B-clamp ring for DNA insertion
(“sliding clamp”) inner surface is optimized for transient interaction with DNA
the B-clamp tethers pol III to DNA, increasing processivity of pol III
