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Midterm 1 Flashcards

1
Q

What is the difference between a selectable and screening marker

A

a selectable marker tells you if plasma is inside the bacteria (antibiotic resistance genes) while a screening marker tells you if insert is inside the plasma (blue- white screening method)

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2
Q

Which vector is more efficient, bacteriophages or plasmids

A

bacteriophages

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3
Q

Which enzyme can we use to prevent self ligation

A

alkaline phosphatase

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4
Q

which end of dna is potentially ambiguous in length during pcr replication

A

3’ prime end

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5
Q

When does DNA absorb the most light

A

highest degree of separation

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6
Q

what correlates with increasing Tm

A

increasing GC content due to the number of hydrogen bonds ( has 3 while AT only has 2)

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7
Q

What are the steps to RT-PCR

A
  1. start with mrna
  2. reverse transcriptase
    3.use foward primers to convert ssDNA to dsDNA
  3. proceed with regular PCR
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8
Q

What is at the 5’ prime end of dna

A

phosphate

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9
Q

What is the difference between RNA and DNA (structurally)

A

RNA has an OH group in the 2’ position
DNA is missing this group

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10
Q

what is a nucleoside

A

base+sugar

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11
Q

what is at the 3 prime end of DNA

A

OH

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12
Q

What are the conditions needed to denature DNA

A

low salt environment, alkali conditions, or heat

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13
Q

How does a low salt environment help denature DNA

A

positive cations (Na+) can alleviate some of the negative repulsion of the phosphate background. The lack of these cations causes instability

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14
Q

Does DNA denaturation happen all at once

A

No, regions of DNA differ in GC content and thus will denature at different rates

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15
Q

What temp is best for renaturation of DNA strands

A

25 below Tm

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16
Q

What are the primary factors for degree of renaturation

A

DNA concentration, 25 below TM Temp, and time

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17
Q

What are heteroschizomers

A

Recognize the same site but cut in different regions

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18
Q

How do host bacteria prevent their dna from being cut up

A

Methylation

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19
Q

How does methylation work when replication occurs

A

Semi conservative replication so one strand is methylated while the other is not. This still protects the strand until the other methyl group is added by methylase

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20
Q

How is DNA ligase activated and what does it do

A

AMP and facilitates a phosphodiester bond between 5’ end and 3’ of DNA fragment

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21
Q

What are the two methods used to transform DNA

A

calcium neutralization of phosphate backbone
electroporation of host membrane

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22
Q

LacZ is only active as a

A

homotetramer

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22
Q

What are the desirable characteristics of a cloning vector

A

origin of replication, multiple cloning sites, and selectable marker

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23
Q

What kind of colonies will you get if the insert is properly inserted into LAC-z operon

A

white

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24
Which vector type is more efficient (phage or plasma)
phage
25
which vector forms plaques
bacteriphages due to the lysis of cells
26
What are the ingredients of a PCR reaction
dNTPS, thermostable DNA polymerase, target DNA, primers, and Mg2+ ( cofactor for DNA polymerase)
27
What is special about ddTTP
it lacks a OH at the 3 group position. Whenever it is incorporated by a DNA polymerase the chain will stop
28
which enzyme has bidirectional exonuclease activity
Polymerase 1
29
which enzyme produces RNA primers
primase
30
which polymerase is responsible for removing rna primers
polymerase 1
31
Which polymerase is most closely associated with replication
Polymerase 3
32
What does DNAa forming a complex with
The HU protein and ATP
33
where does the DNAa complex bind to
the 9mers regions
34
What does DNAc do
helps guide/deliver DNAb to open complex region
34
what is the structure of DNAb
hexamer
34
what is the product of DNAa complex binding
13mer region begins to melt which allows for binding of DNAb
34
what is the function of SSB proteins
these proteins help keep strands separated
35
which dna subtype is a helicase
DNAb
36
what is the function of topoisomerase
relieving tension in DNA strands as they are unwinded
37
What is an example of a type 2 topoisomerase
gyrase
38
How does dna gyrase work
cuts both strands and then rejoins them to relieve tension
39
What causes alkylation of bases
electrophiles attacking electron rich centers and attaching an alkyl group
40
What are three types of alkylation
N7, N3, and O6
41
Considered to be a generally harmless form of alkylation
N7 of guanine
42
Creates a base that cannon pair with any other nucleotide (alkylation)
N3 of Adenine
43
Changes a GC to a AT pair (alkylation)
O6 of Guanine
44
Form of radiation that results in pyridimine dimers (T-T bonding)
UV rays
45
Radiation capable of breaking DNA strands
X-rays/Gamma rays
46
How does the body repair damages caused by UV rays
photolyase (activated by light) is able to break the bonds between pyridimine bases
47
Which enzyme can undo 06 Guanine damage
The suicide enzyme/methylguanine methyltransferase
48
How does base excision repair work
DNA glycosylase extrudes bases and removes, AP endonuclease cuts where base was, DNA phosphodiesterase removes phosphate, polymerase 1 adds nucleotide with 5 to 3'
49
How does NER work
Excinuclease cuts out section of DNA, Polymerase 1 fills in bases, and DNA ligase seals the knicks
50
DNA glycosylase function
remove errant base in BER
51
phosphodiesterase function
removal of phosphate group
52
What is the difference between homologous and nonhomologus end joining
homologous end joining uses a sister chromatid as a template for repair
53
What are the two problems that linear chromosomes present
1. differentiating strand breaks and the end of chromosomes 2. Ends of DNA being cleaved during replication
54
What are telomeres rich in
G content
55
What is the telomere repeat sequence in humans
TTAGGG
55
What kind of enzyme is telomerase
reverse transcriptase enzyme
56
What kind of TE does TN10 use
non replicative
57
What are class 1 TE's (in eukaryotes)
A class of TE'S that use reverse transcriptase to produce new copies that insert at new locations in the genome
58
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Bio 107 (2 decks)

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