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Bio 107 > Midterm 1 > Flashcards

Midterm 1 Flashcards

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Biology 101 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
Q

Which vector type is more efficient (phage or plasma)

A

phage

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25
Q

which vector forms plaques

A

bacteriphages due to the lysis of cells

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26
Q

What are the ingredients of a PCR reaction

A

dNTPS, thermostable DNA polymerase, target DNA, primers, and Mg2+ ( cofactor for DNA polymerase)

27
Q

What is special about ddTTP

A

it lacks a OH at the 3 group position. Whenever it is incorporated by a DNA polymerase the chain will stop

28
Q

which enzyme has bidirectional exonuclease activity

A

Polymerase 1

29
Q

which enzyme produces RNA primers

A

primase

30
Q

which polymerase is responsible for removing rna primers

A

polymerase 1

31
Q

Which polymerase is most closely associated with replication

A

Polymerase 3

32
Q

What does DNAa forming a complex with

A

The HU protein and ATP

33
Q

where does the DNAa complex bind to

A

the 9mers regions

34
Q

What does DNAc do

A

helps guide/deliver DNAb to open complex region

34
Q

what is the structure of DNAb

A

hexamer

34
Q

what is the product of DNAa complex binding

A

13mer region begins to melt which allows for binding of DNAb

34
Q

what is the function of SSB proteins

A

these proteins help keep strands separated

35
Q

which dna subtype is a helicase

A

DNAb

36
Q

what is the function of topoisomerase

A

relieving tension in DNA strands as they are unwinded

37
Q

What is an example of a type 2 topoisomerase

A

gyrase

38
Q

How does dna gyrase work

A

cuts both strands and then rejoins them to relieve tension

39
Q

What causes alkylation of bases

A

electrophiles attacking electron rich centers and attaching an alkyl group

40
Q

What are three types of alkylation

A

N7, N3, and O6

41
Q

Considered to be a generally harmless form of alkylation

A

N7 of guanine

42
Q

Creates a base that cannon pair with any other nucleotide (alkylation)

A

N3 of Adenine

43
Q

Changes a GC to a AT pair (alkylation)

A

O6 of Guanine

44
Q

Form of radiation that results in pyridimine dimers (T-T bonding)

A

UV rays

45
Q

Radiation capable of breaking DNA strands

A

X-rays/Gamma rays

46
Q

How does the body repair damages caused by UV rays

A

photolyase (activated by light) is able to break the bonds between pyridimine bases

47
Q

Which enzyme can undo 06 Guanine damage

A

The suicide enzyme/methylguanine methyltransferase

48
Q

How does base excision repair work

A

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
Q

How does NER work

A

Excinuclease cuts out section of DNA, Polymerase 1 fills in bases, and DNA ligase seals the knicks

50
Q

DNA glycosylase function

A

remove errant base in BER

51
Q

phosphodiesterase function

A

removal of phosphate group

52
Q

What is the difference between homologous and nonhomologus end joining

A

homologous end joining uses a sister chromatid as a template for repair

53
Q

What are the two problems that linear chromosomes present

A
  1. differentiating strand breaks and the end of chromosomes
  2. Ends of DNA being cleaved during replication
54
Q

What are telomeres rich in

A

G content

55
Q

What is the telomere repeat sequence in humans

A

TTAGGG

55
Q

What kind of enzyme is telomerase

A

reverse transcriptase enzyme

56
Q

What kind of TE does TN10 use

A

non replicative

57
Q

What are class 1 TE’s (in eukaryotes)

A

A class of TE’S that use reverse transcriptase to produce new copies that insert at new locations in the genome

58
Q
A
59
Q
A
60
Q
A

Bio 107 (2 decks)

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