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MOL BIOLOGY > DNA structure and basics > Flashcards

DNA structure and basics Flashcards

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1
Q

scientific name of ADENINE

A

6 amino purine

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2
Q

scientific name of thymine

A

2,4-dioxo-5-methyl pyrimidine

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3
Q

scientific name of cytosine

A

4-amino-2 oxo pyrimidine

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4
Q

scientific name of uracil

A

2,4-dioxopyrimidine

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5
Q

what is chargaffs rule and what does it indicate if it is not being followed

A

py = pu

if chargaffs rule is not being followed then most probably it is a single stranded DNA.

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6
Q

write down the characteristics of the PDB backbone

A

the pdb bond is ionisable and lends to the acidic nature of the DNA and therefore gives rise to the negative backbone

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7
Q

what is the most important interaction of the DNA structure

A

base stacking

it helps in keeping the h bond linear

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8
Q

How do you disrupt the base stacking structure?

A

urea,
formaldehyde,
acridine orange,
EtBr

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9
Q

glycosidic bond can be disrupted by

A

glycosylase and extreme NaOH

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10
Q

how do you break the phosphodiester bond?

A 
endonuclease,
.
.
.
exonuclease
specific RE
non specific dnase1
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11
Q

what are the types of topoisomerase and what are there functions

A

type 1 and type 2

type 1 breaks 1 strand only and

type 2 breaks 2 strands

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12
Q

what are the conditions for denaturation of the DNA

A

High temperature
low salt concentration
high ph value
disruption of the base stacking

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13
Q

what are the conditions for the renaturation of the DNA

A
  1. tempr must be about 25-30 degrees lower than the denaturation temp.
  2. salt concentration
  3. size of the fragments
  4. Conc. of renealling fragments
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14
Q

what type of reaction is denaturation and the renaturation of DNA

A

denaturation: 1st order reaction
renaturation: 2nd order reaction

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15
Q

sequence of reactions for 5’ labelling

A
  1. treat with phosphatase which will lead to the removal of alpha phosphate
  2. phosphorylation with the help of Gamma 32 labelled phosphate ATP with the help of KINASE.
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16
Q

sequence of reactions for the 3’ labelling

A

use of alpha p32 labelled along with TDT

17
Q

what happens if glycosidic bond is broken down

A

AP condition will be formed
Apurinic
Apyrimidinic

18
Q

what if dna is treated with strong acid?

A

acidic treatment leads to AP CONDITION

19
Q

what if DNA is treated with strong base?

A

ALkali treatment

hydrolysis

deprotonation

tautomerisation

ketoenol formation

denaturation

20
Q

eg. of crosslinking agents

A

Psorlan
Mitomycin C
nitrogen and sulphur mustard
cis platin

21
Q

what happens with the use of crosslinking reagents

A

cells will die

as the opposite strands will get attached and it would lead to halt in DNA replication fork

22
Q

where is positive supercoiling seen and what do they have in exception

A

T even bacteriphages

they have 5 HMC in place of Cytosine

23
Q

what is the condition corresponding to the hypochromic or hyperchromic shift?

A

when there is a change in the amount of molecule

24
Q

what are conditions corresponding to the bathochromic shift or hyprochromic shift?

A
  1. change in proprety of molecules

2. surrounding of molecule

25
Q

what does the Tm analysis represent?

what are the factors that the Tm of the DNA depends upon?

A

stability of the DNA

Tm is dependent upon:

  1. salt conc.
  2. pH concentration
  3. proteins
  4. Interchelating agent
  5. GC content
26
Q

what does the area under the renaturation curve represent

A

size of the genome

27
Q

what does the slope of the renaturation curve represent

A

repetetiveness of the genome.

28
Q

where are conservative and dispersive replication seen?

A

dispersive : seen in some viruses

conservative: organelles

29
Q

In prokaryotes which DNA pol is responsible for the 5’-3’ exonuclease activity

A

POL 1

30
Q

which enzyme is used to break down the POL 1

A

subtilisin/trypsin

31
Q

when treated with subtilisin the enzyme is broken down into

A

smaller fragment which has 5’-3’ exonuclease activity and the larger klenow fragment

32
Q

what are the core subunits of the DNA pol III

A

alpha (polymerase activity)
epsilon (exonuclease activity)
theta

33
Q

accessory subunits of the DNA pol III

A

Tau: required for initiation

gamma: Clamp loader
beta: Sliding clamp

Delta: recycling of the sliding clamp

delta’/psi: association of gamma

34
Q

eukaryotic polymerase that is used in organelle replication

A

pol gamma

35
Q

pol that is used in lagging strand synthesis

A

alpha and delta

36
Q

pol that is used in repair mechanisms

A

beta

37
Q

size of okazaki in prokaryotes and eukaryotes

A

1000-2000

100-200

38
Q

by which method was the okazaki fragments first discovered?

A

sucrose density gradient centrifugation

MOL BIOLOGY (1 decks)

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