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MCBM Part 1 > Kandpal - DNA Replication > Flashcards

Kandpal - DNA Replication Flashcards

1
Q

With hybridization , how many fragments of DNA can be hybridized?

A

Two

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2
Q

What is Southern hybridization?

A

Probe fragment to a DNA fragment

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3
Q

What is Northern hybridization?

A

Probe fragment to a RNA fragment

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4
Q

What does PCR stand for?

A

polymerase chain reaction

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5
Q

What are the requirements for PCR?

A
  1. Template
  2. Pair of primers
  3. 4 Deoxyribonucleotides
  4. Taq DNA polymerase
  5. Appropriate buffer
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6
Q

What are the 4 deoxyribonuceotides?

A

dATP, dGTP, dCTP and dTTP

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7
Q

What is the cycling process called in PCR?

A

Exponential amplification 2^n
Note: Denaturation occurs at 95 degrees Celsuis.
Note:DNA strand extension at optimum temp of Taq 72 degrees Celsius

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8
Q

What is separates the DNA strands?

A

Heat

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9
Q

What is added during step 2 in the PCR process?

A

Hybridization of primers

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10
Q

What occurs during step 3 of PCR?

A

DNA synthesis

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11
Q

If you have 2 cycles of replication, how many DNA strands will you have in total

A

4 double stranded molecules

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12
Q

What is microarray based hybridization?

A

Determing expression of genes in 2 tissues by using a poll of probes

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13
Q

What chemical could be used during microarray testing?

A

Fluorchrome

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14
Q

If you have the color yellow during microarray, what does it display?

A

Both genes are being expressed by both RNA

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15
Q

If you have the color red during microarray, what does it display?

A

The sample of 1 is being expressed.

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16
Q

If you have the color green during microarray, what does it display?

A

The sample of 2 is being expressed

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17
Q

During a paternity test, what are you trying to match?

A

Matching Allele based markers

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18
Q

Is the alleged father the real father, if yes or no, how can one conclude it?

A

Consider allele frequencies

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19
Q

What does VNTR stand for?

A

Variable Number of Tandem Repeats

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20
Q

What is the function of VNTR?

A

Repeated units of that are short(microsatellites), intermediate (minisatellites) or large

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21
Q

T or F, Using one marker will not provide a statistically signficant match?

A

False, match of a multiple markers can allow a conclusion of a statistically significance similarity between two samples.

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22
Q

Do prokaryotes and eukaryotes fallow the same general principles of replication?

A

YES!

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23
Q

What major therapeutics give application of molecular differences?

A

Antibiotics

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24
Q

What states that “Every cell in the body arises from an existing cell”?

A

The Cell doctrine

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25
Q

What phase of DNA replication is the longest in time?

A

Interphase

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26
Q

What phase to sister chromatids seperate and go to opposite sides to their poles?

A

Anaphase

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27
Q

What is the basis of Meiosis?

A

Replication + 2 rounds of cell division

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28
Q

What can cause mutation to disease?

A

During cyclin kinases

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29
Q

What are the 3 checkpoints?

A
  1. DNA replicates only when conditions are right.
  2. Mitosis occurs only after replication has completed.
  3. Cytokinesis occurs only after all chromosomes have separated.
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30
Q

If each DNA strand during replication serves as a template to specify its complementary strand, what is this called?

A

Semiconservative

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31
Q

DNA polymer extends in what direction always?

A

5’ to 3’

32
Q

What is DNA polymerase type 1 for E. coli?

A

Low processivity (DNA repair)

33
Q

What is DNA polymerase type 2 for E. Coli?

A

Somewhat higher processivity (DNA repair)

34
Q

What is DNA polymerase type 3 for E. Coli?

A

Highest processivity (DNA replication)

35
Q

What is processivity?

A

Continue to synthesize due to the fact it can replicate by latching back to the a new strand.

36
Q

Out of the 3 polymerase for E. Coli, which one is part of replicase?

A

Pol 3.

37
Q

Out of the 3 polymerase for E. Coli which one has 3 activities compared to the others, which have 2.

A

Pol 1 has three.

38
Q

Name the 6 bacterial protiens and their gene names.

A
  1. dnaA Initiator protein
  2. dnaB Helicase
  3. dnaG Primase
  4. polA Polymerase I
  5. polB Polymerase II
  6. dnaE Polymerase III
39
Q

T or F, DNA has parallel polarity?

A

False, Antiparallel polarity

40
Q

What happens when a wrong base is incorporated?

A

DNA Polymerase has an editing (exonuclease) activity

41
Q

What is the error frequency after proofreading E. Coli?

A

10-9.

42
Q

What is the genome size basepairs for E. Coli?

A

Genome size 4.64 x 106 basepairs

~5 x 10-3 errors per replication cycle

43
Q

How large is the HUMAN genome in basepairs?

A

3.2 x 10-9 basepairs

44
Q

T or F, A nucleotide cannot be completed if the base pair is incomplete?

A

True.

45
Q

What is the error rate for the Human genome?

A

Approx. 3/cell/replication

46
Q

How many cells do humans have and what is the percentage in coding DNA?

A

10^14 cells and the Approx 1% is coding DNA

47
Q

Replication begins at which point in order to start replication?

A

Origin of replication

48
Q

T or F, Initiator protein (dnaA) binds to the origin and denatures A-T base pairs?

A

True.

49
Q

What type of helicase unwinds the double stranded DNA?

A

dnaB (ATP dependent)

50
Q

What relieves overwinding of DNA?

A

Type 2 topoisomerase (gyrase in E. Coli)

51
Q

T or F, DNA cannot start without a primer?

A

True

52
Q

How long is the primase synthesis nucleotide?

A

15 nucleotides long

53
Q

DNA polymerase 3 adds new nucleotides to which side?

A

3’ OH end

54
Q

T or F, 5’ to 3’ is where polymerase 1 will remove the RNA sequence?

A

True

55
Q

What energy is released during step 2 of DNA ligase?

A

AMP

56
Q

What energy is used during DNA ligase?

A

ATP

57
Q

Polymerase 3 is part of a hugh part of replication, what is another name for Polymerase 3

A

Holoenzyme

58
Q

What are the 4 main key subunits of holoenzyme

A
  1. Catalytic core of three subunits a-e-q,
  2. Clamp subunits (b, b) for processivity
  3. Clamp loader (g complex)
  4. Assembly subunit (t, t)
59
Q

What lays does the DNA helicases?

A

Kinase

60
Q

IN THIS LECTURE GO OVER SLIDE 41 FOR BETTER CLARIFICATION ON E. COLI REPLICATION

A

……

61
Q

Why do we look at E.Coli for information?

A

The replication principle is the same for mammalian E.Coli cells, leading to potential creation of antibiotics.

62
Q

What is a logical target for inhibiting bacterial life process?

A

Enzymes of DNA replication

63
Q

What type of microbes produce aminocoumarin class of antibiotics like “Novobiocin”?

A

Streptomyces spheroides and Stretpmyces niveus

64
Q

What are synthetic antibiotics for replication and transcription?

A

Levofloxacin and Ciprofloxacin

65
Q

True of False, Type 1 Topoisomerases will cut one strand of DNA?

A

True.

66
Q

True of False, Type 2 Topoisomerases will cut 1 strand?

A

False, it cuts 2.

67
Q

What is another definition of Positive super coiling?

A

Overwound

68
Q

What is another definition of Negative supercoiling?

A

Underwound

69
Q

What is the target enzye for fluoroquinolones?

A

Bacterial Gyrase (Topoisomerase Type 2)

70
Q

Is Gyrase a homotetramer or heterotetramer?

A

Heterotetramer (GyrA2 and GyrB2)

71
Q

T or F, GyrB carries out ATP hydrolysis?

A

True

72
Q

Which one out of Fluoroquinolones or Novobiocin, prevent the reversible ligation step carried out by GyrA?

A

Fluoroquinolones. Novobiocin complete with ATP for binding to GyrB.

73
Q

What drug, FDA approved, used for small cell lung cancer and ovarian cancer?

A

Topotecan (Hycamtin)

74
Q

Name some causes of antibiotic resistance?

A
  1. Bacterial Genomes are small
  2. Replication and doubling times are shorter
  3. Errors in replication are likely to occur
  4. Errors lead to mutations and produce mutant bacteria
75
Q

T or F, Mutant bacterium will be selected and the susceptible bacteria will perish.

A

True

76
Q

What are 2 resistances to Quinolone?

A
  1. N-terminal end of GyrA (most mutations)

2. C-terminal end of GyrB (few mutations)

MCBM Part 1 (29 decks)

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