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135 Cards in this Set

  • Front
  • Back
genome organization for prokaryotes
circular
genome organization for eukaryotes
linear
Bacterial DNA is ___ to increase accessibility to proteins involved in replication or transcription
negatively coiled
Bacterial chromosome is localies to the ___
nucleoid
DNA folded into loops anchored in nucleoid is held in place by ___ and ___
RNA and proteins
Positive supercoiling
in the direction of the helix-- overwound
Negative supercoiling
against the direction fo the helix-- underwound
small circular DNA
plasmids
3 types of plasmids
1. F-factor
2. R-factor
3. COl factor
__ condenses into chromosomes
Chromatin
Bead + DNA =
nucleosome "Beads on a string"
Histone
octamer
2 types of chromatin
1. Euchromatin
2. Heterochromatin
the nuclear envelope contains 2 membranse separated by a ___
perinuclear space
transcriptivly active
Euchromatin
Transport through the nuclear pore complex requires ___
enegry (GTP hydrolysis)
short repeating DNA one after the other
Tandemly
longer repeating DNA scattered
interspersed
Topoisomerase
Type I - single stranded knicks

Type II- double stranded breaks
DNA is folded into loops and anchored in nucleoid. What releases the loops?
RNase
What relaxes the supercoiling but does not release the loops?
Topoisomerase
Proteins that are bound to supercoiled DNA in prokaryotes are analogous to ___ in eukaryotes
histone proteins
Chromatin fibers
DNA bound to proteins
what is revealed when the chromatin is opened up?
beads on a string
histones are connected by what?
thing filament of DNA
The inner membrane of the nuclear envelope rests on a ___ while the outer memebrane is continuous with ___
nuclear lamina, ER
The nuclear pore complex is made up of __ subunits (nucleoproins) that project into the cytoplasm and nucleoplasm
8
when proteins are imported into the nuclear pore complex __ binds to the importin releasing the protein
Ran
meshwork of fibers lining the inner nuclear membrane
nuclear lamina
special intermediate filaments
lamins
special intermediate filaments that may form attachments with inner membrane proteins and may also provide attachment sites for chromatin
lamins
two types of heterochromatin
1. constituative
2. facultative
highly condensed at all times
constituative herterochromatin
cell type specific heterochromatin
facultative
most DNA bound as ___
heterochromatin
chromatin occupies territories near the ___ of the nucleus
periphery
site of ribosome synthesis
nucleolus
genes for rRNA are present on multiple chromosomes but are active only in the nucleolus
Nucleolar organizing region
DNA replication is ___
semiconservative, N1trogen isotope experiment
Ori
site of replication initiation
Bacteria have __ ori
single
site where DNA duplex is replicated
replication fork
replication is
bidirectional
there are ___ sites of DNA synthesis in eukaryotes
multiple
one unit of replication
replicon
what makes a replication origin?
ORC (origin replication complex) and MCM (mini chromosome maintenance comples) bound together mediated by helixase loaders
why A-T rich region?
2 bonds for A-T vs 3 bonds for G-C
Autonomously replicating sequences are present in ___
yeast
__ replication forks per origin that go bidirectionally and fuse
2
DNA synthesized at forks by what?
DNA polymerase
growth is in what direction?
5' to 3'
what end is the lagging strand?
5' end
how do you add to the lagging strand?
okazaki fragments
why is there no 3' to 5'?
1. DNA polymerase proofreads
2. 5' proofreading would remove high energy triphosphate
the primer is ___ synthesized by ___
RNA, primase
What can initiate new strand synthesis?
primase
why is the primer RNA?
because if it were DNA it could no longer proofread
removal of high energy __ prevents 3' to 5' synthesis
phosphate
DNA polymerase requires what?
a template
What unwinds DNA at the replication fork?
DNA helicases
what keeps DNA unwound?
single-stranded DNA binding protein
creates knick to relax DNA
topoisomerase
DNA replication complex that moves in the direction of replicaiton fork; causes lagging strand template to loop
replisome
occur spontaneously or in respone to encironmental agents (mutagens)
mutations
what are the two types of mutations?
somatic and germline
what type of mutation is passed to offspring?
germline
this type of mutation can cause cancer?
somatic
what are the two types of spontaneous mutations?
depurination and deamination
loss of a purine by hydrolisis of glycosidic bond linking purine to deoxyribose
depurination
removal of the amino group from a base
deamination
in this type of mutation cytosine is converted into uracil which acts like thymine (it pairs with adenine)
deamination
3 chemical mutagens
1. Base analogs
2. Base modifying agent
3. Intercalated agents
what can incorporate into DNA and base pair with different bases?
Base analogs
alter base structure
base modifying agent
insert themselves between adjacent bases; cause distortion in helix
intercalating agents
UV radiation is an environmental mutagen that induces
Thymine dimers
In a thymine dimer the thymens are bound by what type of bond?
covalent
___ synthesis of new DNA where the template is damaged
translesion
what prevents that passage of initial mutations to a newly forming DNA strand
damage tolerance
explain excision repair
endonuclease cuts out damage; DNA pol fills in missing nucleotides; DNA ligase seals the knicks
what type of repair corrects single damaged bases?
Base excision
deaminated bases are detected by what?
DNA glycosylase
what type of repair recognizes distortions in DNA?
Nucleotide excision repair
what are the two ways to repair a thymine dimer?
translesion and nucleotide excision
methylation
proves which strand is the existing strand
this type of repair targets erros made during replication that are not corrected by proofreading
mismatch repair
newly synthesized DNA is not yet ___
methylated
Thymine is important in DNA because it can be ___ whereas uracil cannot.
methylated
when two strands of brokne DNA are joined they are error prone and are known as...
non-homologous end joining
cells have 2 copies of each chromosome; when breaks in one copy can be repaired using the second copy as the template it is known as...
homologous recombination
short repeating sequences at endo of each chromosome
telomere
generated additional copies; RNA- containing protein; RNA sequence is complementary to telomere sequence.
Telomerase
rapidly dividing cells spend little time in what phase?
G1/G2
what phase does DNA synthesis occur?
S
what factors influence the start transition?
nutrient availability, cell size and growth factors
what factors influence the G2-M transition?
cell cycle can be arrested in G2 if division is not necessary
what factors influence the Metaphase-Anaphase transition?
proper separation of sister chromatids
what demonstrated the presense of cell cycle control molecules?
heterokaryons
cdks are only active when bound to what?
cyclin
__ cyclins are required for start?
G1
__ cyclins are required for replication?
S
cyclin concentration ___ during cell cycle
oscillate
what was evidence for cell cycle control by cyclin? also induces trasition
Maturation promoting factor (MPF)
___ is a cdk-cyclin complex
MPF
how is cdk activity regulated?
cyclin and phosphorylation
promotes the separation of sister chromatids and degrades mitotic cyclin
Anaphase promoting complex
halt cell cycle until suitable conditions prevail
checkpoints
inhibits Cdc20 and indirectly inhibits APC
MAD/Bub complex
ensures DNA replication had been completed prior to G2-M transition
DNA replication checkpoint
ensures damaged DNA is repaired before cell cycle continues
DNA damage checkpoint
activates puma which initiates apoptosis
P53
what are the four types of RNA?
1. mRNA
2. rRNA
3. tRNA
4. small RNA
DNA and RNA are in what orientation?
antiparallel
2 alpha and 2 beta subunits with the sigama factor form what?
holoenzyme
ensures initiation at proper site on DNA
holoensyme
what binds to the promoter sequence in transcription?
RNA polymerase
the first base transcribes which is usually an adenine is known as what?
start point; +1
-10 sequence
pribnow box
4 steps of transcription
1. binding
2. initiation
3. elongation
4. termination
binds sequence 50-90 bases near 3' end of RNA
Rho factor
What are the two ways termination can occur?
Rho factor
GC rich complementary region
How many RNA polymerases do Enukaryotes use? prokaryotes?
3, 1
in eukaryotes what is analogous to the pribnow box of prokaryotes?
tata box
located in nucleolus and is involved in the synthesis of rRNA precursors
RNA polI
located in the nucleoplasm and is involves in the synthesis of pre-mRNA and nuclear RNA for post transcriptional processing
RNA polII
located in the nucleoplasm and is involved in the synthesis of tRNA
RNA polIII
increase the levels of RNA expression
enhancers
promotes histone disassembly
nucleoplasmin
termination signal
AAUAAA
RNA processin gis type specific. What are the types?
rRNA> tRNA> mRNA
a small subunit and a large subunit make up...
ribosome
multiple RNAs cleaved froma single transcription unit
rRNA
__ blocks methylation and prevents mature rRNA from forming
cycloleucine
sequences in promary transcript that are removed from funtional mRNA
introns
what demonstrate introns?
r looping and restriction enzymes