Exam 1 Flashcards
what is the difference between DNA and RNA
RNA has a 2’ OH group that allows it to form tertiary structures
what are the purines and how many cyclics do they have
adenine, guanine (2)
what are the pyrimidines and how many cyclics do they have
cytosine, thymine, uracil (1)
which purine has a double bonded O group on carbon 6
guanine
which pyrimidine has a NH2 group on carbon 4
cytosine
which C in purines forms the bond with pentose
carbon 9
which C in pyrimidines forms the bond with pentose
carbon 1
what is the name of the bond that connects the phosphate group to the pentose
phosphodiester
what is the name of the bond that connects the pentose to the base (A,T,G,C)
glycosidic
describe chargaffs rules
number of purines (A+G) = number of pyrimidines (T+C)
the relative ratios between purines and pyrimidines stays constant between different tissues of an individual
DID NOT SAY that T and A pair together and G and C pair together
what base pair combo will result in a higher melting point
G-C
what is the difference between ddNTP and dNTP
ddNTPs lack a 3’ OH
ddNTPs used to stop
dNTPs used to start
what are ddNTPs used for
sanger sequencing
5’ AAC GGT ………….. TAA CTG 3’
what are the primers that should be used for this fragment of DNA
left primer 5’ AAC GGT 3’
right primer 5’ CAG TTA 3”
what is the difference between a mutation and a SNP (polymorphism)
a mutation is present in less that 1% of the population
what contributes to a 30nm filament
histone H1
histone tails
NOT INCLUDED: chromatin remodeling complexes
what are three ways chromatin remodeling complexes modulate gene expression
insert, eject, move nucleosomes
what is the light part of a cell called (open)
euchromatin
what is the dark part of a cell called (closed)
heterochromatin
what is the function of H3.3
lock DNA in open confirmation
what is the function of H2A.X
recruitment of DNA repair proteins
what is the function of macroH2A.Z
inactivation of X chromosome in female cells
what is the function of CENPA
binds kinetochores
is bromodomain protein associated with open or closed chromatin
open
is acetylation of histone tails associated with open or closed chromatin
open
is methylation of histone tails associated with open or closed chromatin
closed
is high nucleosome density associated with open or closed chromatin
closed
what does pol III - polymerase domain do
performs DNA replication
what does helicase do
unwinds DNA duplex
what does the clamp loader do
loads the beta sliding clamp
what does primase do
synthesizes RNA primer
what does topoisomerase do
removes topological stress
what does pol III 3’ to 5’ exonuclease domain do
removes mismatched nucleotides (proofreading) during replication
what does the delta subunit of the clamp loader do
removes beta clamp after replication
what does ligase do
catalyzes phosphodiester bond between okazaki fragments (during replication)
what remains on the DNA at the end of replication of a okazaki fragment
beta sliding clamp
what is released from the DNA at the end of replication of a okazaki fragment
pol III
what enables the removal of the RNA bases and addition of dNTPs on the okazaki fragment after it is replicated
pol I 5’ to 3’ exonuclease activity
the simultaneous RNA removal and DNA synthesis is called
nick translation
what is the difference between a PCR and a rtPCR
PCR: amplifies DNA sequence
rtPCR: measures amount of DNA
1 nucleosome is composed of what histones
2x
H2A, H2B, H3, H4
1 nucleosome is composed of what histones
2x
H2A, H2B, H3, H4
how are histones modified
specialized histone modifying enzymes
some enzymes add modifications, some remove them
is new or old DNA heavier
old DNA –> heavier
what is the replisome
all proteins that work together during DNA replication elongation
what is contained in the pol III holoenzyme
pol III core, beta sliding clamp, clamp loader
what is the role of the pol III core
all nucleotides and proofreading
what is the role of the beta sliding clamp
increase speed of replication
what is the role of SSB
protects ssDNA
what are the initiation steps of replication in bacteria
- 9mer repeats bound by DnaA
- torque destabilizes DNA so DNA opens at 13mer repeats
- using the prepriming cortex, replication bubble opens more
- primers are made
- holoenzyme does replication on both leading strands until it reaches opposite side of bubble
- holoenzyme docks
- regular replication starts on both strands
what is a DAM site
GATC, A gets a methyl group added
what is it called when on of the two strands is methylated
hemimethylated DNA
what is the role of seqA
seqA recognizes hemimethylated DNA and prevents binding of DnaA –> no replication
how is replication regulated so that a second initiation does not occur too early
after seqA binds, DAM starts methylation of the new DNA strand; by the time DAM has methylated all of the DAM sites, the entire chromosome is replicated
what would happen to replication if DAM was inhibited
replication initiation would not happen
what are the steps of the cell cycle
- G1: assembly of the pre-replication complex
- S-entry: degradation of preRC
- S: assembly of replication complex
what happens to replication if cdt1/cdc6 do not remain degraded
replication would re-initiate before the previous cycle of replication has finished
