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Flashcards in Kandpal - DNA Replication Deck (76):
1

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

Two

2

What is Southern hybridization?

Probe fragment to a DNA fragment

3

What is Northern hybridization?

Probe fragment to a RNA fragment

4

What does PCR stand for?

polymerase chain reaction

5

What are the requirements for PCR?

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

6

What are the 4 deoxyribonuceotides?

dATP, dGTP, dCTP and dTTP

7

What is the cycling process called in PCR?

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

8

What is separates the DNA strands?

Heat

9

What is added during step 2 in the PCR process?

Hybridization of primers

10

What occurs during step 3 of PCR?

DNA synthesis

11

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

4 double stranded molecules

12

What is microarray based hybridization?

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

13

What chemical could be used during microarray testing?

Fluorchrome

14

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

Both genes are being expressed by both RNA

15

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

The sample of 1 is being expressed.

16

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

The sample of 2 is being expressed

17

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

Matching Allele based markers

18

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

Consider allele frequencies

19

What does VNTR stand for?

Variable Number of Tandem Repeats

20

What is the function of VNTR?

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

21

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

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

22

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

YES!

23

What major therapeutics give application of molecular differences?

Antibiotics

24

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

The Cell doctrine

25

What phase of DNA replication is the longest in time?

Interphase

26

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

Anaphase

27

What is the basis of Meiosis?

Replication + 2 rounds of cell division

28

What can cause mutation to disease?

During cyclin kinases

29

What are the 3 checkpoints?

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.

30

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

Semiconservative

31

DNA polymer extends in what direction always?

5' to 3'

32

What is DNA polymerase type 1 for E. coli?

Low processivity (DNA repair)

33

What is DNA polymerase type 2 for E. Coli?

Somewhat higher processivity (DNA repair)

34

What is DNA polymerase type 3 for E. Coli?

Highest processivity (DNA replication)

35

What is processivity?

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

36

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

Pol 3.

37

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

Pol 1 has three.

38

Name the 6 bacterial protiens and their gene names.

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

39

T or F, DNA has parallel polarity?

False, Antiparallel polarity

40

What happens when a wrong base is incorporated?

DNA Polymerase has an editing (exonuclease) activity

41

What is the error frequency after proofreading E. Coli?

10-9.

42

What is the genome size basepairs for E. Coli?

Genome size 4.64 x 106 basepairs
~5 x 10-3 errors per replication cycle

43

How large is the HUMAN genome in basepairs?

3.2 x 10-9 basepairs

44

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

True.

45

What is the error rate for the Human genome?

Approx. 3/cell/replication

46

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

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

47

Replication begins at which point in order to start replication?

Origin of replication

48

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

True.

49

What type of helicase unwinds the double stranded DNA?

dnaB (ATP dependent)

50

What relieves overwinding of DNA?

Type 2 topoisomerase (gyrase in E. Coli)

51

T or F, DNA cannot start without a primer?

True

52

How long is the primase synthesis nucleotide?

15 nucleotides long

53

DNA polymerase 3 adds new nucleotides to which side?

3' OH end

54

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

True

55

What energy is released during step 2 of DNA ligase?

AMP

56

What energy is used during DNA ligase?

ATP

57

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

Holoenzyme

58

What are the 4 main key subunits of holoenzyme

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

What lays does the DNA helicases?

Kinase

60

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

......

61

Why do we look at E.Coli for information?

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

62

What is a logical target for inhibiting bacterial life process?

Enzymes of DNA replication

63

What type of microbes produce aminocoumarin class of antibiotics like "Novobiocin"?

Streptomyces spheroides and Stretpmyces niveus

64

What are synthetic antibiotics for replication and transcription?

Levofloxacin and Ciprofloxacin

65

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

True.

66

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

False, it cuts 2.

67

What is another definition of Positive super coiling?

Overwound

68

What is another definition of Negative supercoiling?

Underwound

69

What is the target enzye for fluoroquinolones?

Bacterial Gyrase (Topoisomerase Type 2)

70

Is Gyrase a homotetramer or heterotetramer?

Heterotetramer (GyrA2 and GyrB2)

71

T or F, GyrB carries out ATP hydrolysis?

True

72

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

Fluoroquinolones. Novobiocin complete with ATP for binding to GyrB.

73

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

Topotecan (Hycamtin)

74

Name some causes of antibiotic resistance?

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

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

True

76

What are 2 resistances to Quinolone?

1. N-terminal end of GyrA (most mutations)
2. C-terminal end of GyrB (few mutations)