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Molecular > Lect 4 > Flashcards

Lect 4 Flashcards

1
Q

Eukaryotes have multiple ….compared to prokaryotes

A

Ori C

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2
Q

Polymerase a

Polymerase b

Polymerase y

Polymerase €

Polymerase delta

Both

A

Leading strand and each fragment begining on lagging
Primer, 10 nucleotides
Polymerase, 15 bases
5’ to 3’

DNA repair

Mitochondrial DNA

Leading strand elongation

Lagging strand elongation, filling RNA primer gaps after their removal

PCNA aid in ensuring high processivity

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3
Q

What is PCNA

A

Proliferating cell nuclear antigen
Sliding DNA clamp

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4
Q

Do pol € and pol deltA

A

Yes 3’ to 5’ exonuclease activity

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5
Q

Pro vs eu
Primer synthesis
Sliding clamp
Primer removal
Gaps after RNA removal

A

Primase. Pol a
B subunit in pol III, PCNA pol€ and pol sigma
Pol I. FEN1, RNase H
Pol I. Pol delta

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6
Q

Removal of RNA primers

A

RNAse H, RNA hybridase, removes all RNA. primers leaving only 1

Flap endo nuclease 1, FEN1, removes the remaining one and a few nucleotides from 5’ end of okazaki fragment

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7
Q

Why is replication slower in eukaryotes

A

Hampered by nucleosomes

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8
Q

Which has longer okazaki fragments
Which has shorter RNA primers

A

Prokaryotes 1000-2000
Eukaryotes 100-200

Prokaryotes 5
Eukaryotes 10

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9
Q

The multiple ori C of eukaryotes are separated by…. Bp

Ori C site is rich in…..

Areas between ori C are called

A

5k-300k bp

A–T bp

Replicons

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10
Q

Advantages of multiple Ori C

A

Shorter replication time
Compensates for slow action of DNA polymerases

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11
Q

After the removal of the last RNA primer …..forms that cannot be fixed by polymerase delta why…

A

Gap
Can not work on the very end

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12
Q

What are telomeres

Func

They are…repeats….paired to region containing

A

DNA and proteins(sheltrin)

Maintain structural integrity
Prevent nucleases attacks
Allow repair systems to distinguish a true end from a break

Tandem
TTAGGG
C and A

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13
Q

Which strand is longer than the other

A

G rich is longer
3’ overhang

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14
Q

What happens to the 3’ overhang

A

Folds upon itself forming a loop stabalized by sheltrin proteins

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15
Q

Usually in somatic cells the region left by removal of…can not be filled hence …

A

RNA primers
Telomere shortening in each division till cells are senescent

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16
Q

Does telomeres shorten in germ cells, cancer cells and stem cells?

What happens

A

No

Telomerase enzyme comes to the rescue

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17
Q

Telomerase components and their func

A

Tert> protein part acting as reverse transcriptase

Terc> RNA part acting as a template, C rich

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18
Q

Terc template base pairs with…..and Tert uses the…to…

A

G rich strand, 3’ overhang
RNA template
Elongate the already long G rich 3’ overhang

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19
Q

Once the G rich strand is lengthened…..

A

Pol a can use it as a template to synthesis RNA primer by its primase activity then extended
Afterwards removed by nucleases

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20
Q

Telomeres are…
Their length is….to no. Of times the cell have divided

Telomere study provides insights into
….

A

Mitotic clocks
Inversely prop

Normal aging, premature aging, cancer

21
Q

Progerias is

A

Premature aging

22
Q

DNA synthesis in pro vs eu

A

Pro throughout the cell cycle
Eu during S phase only

23
Q

Nucleosomes fate
Histones source

A

During replication nucleosomes are disassembled to allow access of DNA however once the na is formed they quickly reform

Histones either parental or de novo
Randomly distributed

24
Q

When does the synthesis of histones occur

A

During DNA replication

25
Q

Overall differences in replication as a process

A

Eukaryotes are slower
Many Ori C
Shorter okazaki fragments
Longer primers

26
Q

DNA is constantly subjected to….
Types of damaging agents

A

Environmental insults

Chemical> nitrous acid causing deamination
Radiation>
Non ionizing, UV causes pyrimidine dimer
Ionizing , X ray causes double strand breaks

27
Q

If damage is not repaired…..occurs
Leading to…

A

Mutation
Loss of control of proliferation and cancer

28
Q

Main steps for repair

A

1.damage rec
2.removal of damage
3.replacement
4.gap filling
5.ligation

29
Q

Abt…..purines are lost….per day

A

10000
Spontaneously

30
Q

MMR
proteins are ..

A

Mut

31
Q

How mut proteins identify the wrong strand

A

What is the degree of methylation as methylation takes time and it is not done immediately after synthesis.
So the nascent strand is assumed to be wrong and the parental is assumed to be correct.

In eukaryotes by nicks unsealed

32
Q

3’…..5’ methylation on adenine seq by…
Once per…

A

GATC
DAM, DNA adenine methylase
1000 nucleotides

33
Q

The repair

A

SLH
mut S , recognises mismatch and recruits mut L
Mut S and Mut L complex activates Mut H
Mut H cleaves unmethylated daughter strand

34
Q

Mut H acts by …..to cleave damage and….to remove damage and additional nucleotides at…

A

Endonuclease
Exonuclease
5’ end and 3’ end

35
Q

Gap filling at MMR
Joining

A

DNA pol III
Pol €

3’ OH and 5’ p of remaining stretch by ligase

36
Q

Mutation in proteins involved in MMR are associated with…..known as….which has an increased rusk to develop
But MMR mutations are not related to..

A

HNPCC hereditary nonpolyposis colorectal cancer
Lynch syndrome
Colon cancer
Colon cancer only 5%

37
Q

Parental strand methylated and nascent not called…

A

Hemi methylated

38
Q

Uv exposure causes…..preventing….removed by…

A

Pyrimidine dimers 2 adjacent bases covalently bond together
DNA pol action
UvrABC

39
Q

Removal of dimers mainly thymine dimers is called

A

NER, nucleotide excision repair

40
Q

Steps

A

1.Recognition by UvrABC excinuclease activity
2.bulky dimer cleaved from both ends with oligonucleotide containing it
3. Gap filled by Pol I and ligase

41
Q

Defective NER causes

A

Xeroderma pigmentosa
Autosomal recessive disease
Defects in any gene that codes for XP proteins required for NER

42
Q

In XP pyrimidine dimer form…..exposed to….cannot…..resulting in….

A

In skin cells
UV
Repair damage
Extensive accumulation of mutations and cancer

43
Q

Base excision repair BER
Bases alteration reasons

A

Spontaneously like deamination
Or deamination by deaminating compounds

44
Q

Cytosine when deaminated
Adenine
Guanine
5 methyl cytosine

A

Uracil
Hypoxanthine
Xanthine
Thymine

45
Q

Deaminating compounds

A

Nitrous acid which forms precursors like nitrates

46
Q

Steps of BER

A
  1. Abnormal bases like uracil identified by DNA glycosylases
  2. Hydrolytically cleaved from the sugar phosphate backbone
  3. Leaving and apyrimidine or apurine site AP site
    4.AP endonucleases recognize the AP site
47
Q

After AP site recognition

A
  1. Endonucleolytic cut at 5’ end of AP site
  2. Deoxy phosphate lyase removes the sugar phosphate residue
    3.pol I and Pol B fill gaps
  3. Ligase
48
Q

The repairs enzymes

A

MMR> Mut , DAM, SLH
Pol III, pol £

NER> UvrABC
Pol I, pol b

BER> DNA glycosylases , AP endonuclease, deoxyribose phosphate lyase
Pol I, pol b

Molecular (6 decks)

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