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CDB > Cell Nucleus > Flashcards

Cell Nucleus Flashcards

1
Q

How does replication differ between prokaryotes and eukaryotes?

A

1) Initiates at many sites
2) One cycle completed before next starts
3) DNA is assembled into higher order chromatin structure

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2
Q

What specifies origin sites in; viruses, yeast, and higher eukaryotes?

A

1) origin sequence- DNA motif
2) Autonomous replicating sequence(ARS element). Consensus sequence + flanking sequences- DNA motif
3) Probability based in GC rich euchromatic regions. forms G quads, attracts and inherits specific histones and proteins

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3
Q

Why were viruses a model organism for DNA replication?

A

Single origin sequence and initiator protein

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4
Q

How were origin sequences investigated in higher eukaryotes?

A

1) SNS-seq Length based filtering of leading strands, purify with gamma exonucleases that can’t digest RNA primer
2) Init-seq: Transiently intiating replication and filtering for dsDNA. Use antibodies to filter for modified nucleotides

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5
Q

What factors determine higher eukaryotic replication origins?

A
  • Proximity to promoter
  • G rich sequences
  • CpG islands
  • G quadruplexes
  • Histone modifications
  • Open chromatin
  • The associated protein complexes
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6
Q

How does replication avoid clashing with transcription?

A

Go in the same direction

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7
Q

How do centromeres avoid binding the same chromatid?

A

One centromere per chromatid

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8
Q

Why does heterochromatin tend to edges?

A

Pushed out of way, also helps define chromatin borders. But sometimes euchromatin will be close to pores for specific functions

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9
Q

How do you avoid knots in chromatin fiber?

A

Knots require accessible ends. Also binding to nuclear matrix

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10
Q

Does replication and transcription occur at the same time?

A

can be in similar regions but not in the same place

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11
Q

How do nucleosomes with centromere specific histones differ?

A

centromere specific H3 allows binding to kinetochore and recruitment and attachment of proteins related to or part of kinetochore

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12
Q

How do telomeres protect the DNA ends?

A

simple repeat sequence forms terminal hairpin loop, T-loop. Also forms telomere specialized heterochromatin using G quads which attracts sheltrin protein complexes

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13
Q

Why can yeast artificial chromosomes be made?

A

Their ARS can replicate without additional machinery in addition to coding for the centromere attach sites and replicating proteins

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14
Q

What stage and how does the pre-RC assemble?

A
  • G2 phase
  • all origins and backups pre-activated
    1) Origin replication complex
    2) Replication initiator cdc6
    3) Recruitment of 1st Minichromosome maintainance(MCM) with Cdt1
    4) MCM surrounds DNA
    5) Recruit second MCM
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15
Q

How does replication firing occur?

A
  • S phase
  • Happens to both MCM
  • Kinases form the CMG(cdc45, MCM, GINS) complex and start
  • E-CDK2 dephosphrylates cdc6
  • A-CDK2 dephosphorylates cdt1
  • DDK phosphorylates MCM
  • Something phosphorylates ORC
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16
Q

Which strand does helicase displace?

A

5’ end

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17
Q

What do the different DNA polymerases do?

A 
alpha- priming
delta- small steps, okazaki synthesis
epsilon- leads, leading strand
gamma- different, mitochondrial
beta- beta patch, repairs and gap filling
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18
Q

Which polymerases can proof read?

A

delta and eta

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19
Q

What are the proteins needed for DNA replication?

A 
DNA helicase
RPA- single strand binding protein
PCNA- sliding clamp
RFC- loads and unloads PCNA
Fen-1 - removes short primers
Dna2- cut primer flaps
DNA ligase I- Links okazaki fragments
Topoisomerases- Deal with supercoils from splitting strands
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20
Q

How does replication start?

A

1) RPAs attach to ssDNA
2) alpha adds primers then falls off
3) RF-C attaches and recruits PCNA
4) delta attached and starts

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21
Q

How are okazaki fragments matured?

A

delta basically plows through primers and some alpha layed DNA. Then Fen-1 and Dna2 cut off flaps, gap is linked by ligase

22
Q

How do helicases avoid clashes?

A

Opposite strands

23
Q

What is the trombone model?

A

Lagging strand loops around making the lagging and leading strands colinear and allowing a single complex to replicate on both strands(not confirmed for humans)

24
Q

How does topoisomerase I relieve stress?

A
  • Wine

- nicks one strand to allow uncoiling. forms a new ester bond that randomly reattaches to let it do what it wants

25
Q

how are concatenations avoided?

A

Topoisomerase II attaches to two strands, cuts one, passes it through, then ligates. Again a probability based process

26
Q

How are telomeres replicated?

A

RNA template of repeat pattern allows further addition.

27
Q

How do cyclins regulate cell cycles?

A

By activating cyclin dependent kinases which phosphorylated various checkpoints in replication. The cyclins are upregulated at different stages and likely contribute to eachother’s downregulation

28
Q

What is the role of DDK in the cell cycle?

A

Cdc7/Dbf4 kinase complex. Helps phosphorylate the pre-RC

29
Q

How do cells avoid re-initiation?

A

1) Replication license consisting of ORC, Cdc6, Cdt1 and MCM all ATP primed
2) Cyclin-CDKs expressed at different stages for initiating and preventing each step
3) Geminin binds to remaining Cdt1 in S phase

30
Q

How can dormant replication origins help replicate broken DNA?

A

They just help prevent chunks missing due DNA damage boundries, they also fire after DNA repair can start

31
Q

Does polymerase struggle with repeats?

A

No, just a sequencing artifact

32
Q

How is nucleosome code conserved during histone transfer

A
  • Histone recycling with FACT

- Reader-Writer complexes

33
Q

What cyclins fire at what stage?

A

G1: D-CDK4/6, E-CDK2
S: E-CDK2, A-CDK2, Dbf4
G2+M: B/A-CDK1

34
Q

How does the CMG form

A
  • G2 phase
  • GINS+Cdc45 along with other proteins attach as the CMG starts elongation. B-CDK1 is expressed after to prevent inititation in G2
35
Q

How is CMG elongation initiated?

A
  • Initial melting, each CMG releases one strand and clamps the ssDNA with a different opening
  • They start moving in their kissing direction to pass eachther
  • RPAs are deposited
36
Q

How does DNA replication initiation setup?

A
  • Pol alpha is recruited at the RPAs to set down RNA primers
  • RFC attaches to the RNA primers
  • PCNA attaches to RFC and acts as a clamp
  • Pol epsilon or delta attach to the PCNA
37
Q

How are histones transfered during replication?

A
  • MCM bumps into nucleosomes to disassemble them

- FACT sits on MCM or RNA polymerase and holds the components of the nucleosome

38
Q

How does FACT transfer old H3:H4 tetrameres?

A

Pol epsilon: transfers to leading

Pol alpha: transfers to lagging(bc delta not attached)

39
Q

How does FACT transfer old H2A:H2B dimers nucleosomes?

A

Places directly by FACT on leading and lagging

40
Q

What chaperons help transfer new histone components?

A
  • H2A:H2B- NAP1/2

- H3:H4- ASF1 to CAF1

41
Q

How and why are sister chromatin fibers held together

A
  • Cohesins(structural maintainance of chromosomes, SMCs) hold them together
  • This is important for DNA repair mechanisms based on strand invasion
42
Q

How are altered base pairs detected by repair machinery?

A

DNA glycosylase flippes out base pairs then removed the base

AP endonuclease then fixes the missing tooth

43
Q

How is the cells most important DNA efficiently repaired?

A

Nucleotide excision repair is linked to RNA polymerase which stalls at DNA lesions

44
Q

How does nucleotide excision repair work?

A

cleaves both sides of distortion on ssDNA and replaces it

45
Q

What are the 3 types of transposition?

A
  • DNA-only:
    cut-paste, common in bacterial horizontal transfer. leaves behind a hole that may or may not be replaced, important in antibody development
  • Retroviral like:
    Most common in humans, reverse transcriptase and integrase
  • Nonretroviral
    Reverse transcriptase and endonuclease
46
Q

What is “conservative site” specific recombination?

A

Two special sites exchange DNA through transposition. Used by DNA viruses. Can be inverted to turn genes on and off

47
Q

When does the nucleus dissassemble?

A
  • During mitosis in prophase stage
48
Q

What leads to nuclear envelope breakdown?

A

accumulation of cyclin B-CDK1 phosphorylation makes lamina soluable

49
Q

How are proteins localized to the nucleus?

A

Selective phase model.

- molecules interact with gel to get through based on nuclear localisation signals(NLS)

50
Q

How are proteins imported into the nucleus?

A
  • Importin leads to association with pore. With alpha binding the NLS of cargo and beta the pore complex
  • Ran leads to migration through pore
51
Q

Describe the Ran cycle

A

Ran GDP cytosolic, Ran GTP nuclear. This builds up a gradient that leads to transport

  • CAS associates with RanGTP and alpha to enter cytoplasm
  • Alpha binds to beta and NLS to get into nucleus
  • RanGTP transfers beta back to cytoplasm
52
Q

What are two additional methods for protein transport regulation?

A
  • Anchoring which prevents transport until anchor is phosphorylated
  • Shutteling, if the phosphorylation by cyclin B is at a certain level transport becomes unidirecitonal

CDB (13 decks)

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