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DNA > Lecture 5 - PCR > Flashcards

Lecture 5 - PCR Flashcards

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1
Q

what is the basic principle of the PCR reaction

A

polymerase chain reaction

a few pg of DNA is replicated/amplified many times over so we have enough DNA to analyse

we use this to quickly scale up a small amount of DNA to give us enough to analyse

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2
Q

What are the components needed for a PCR reaction (5)

A
  1. template strand
  2. primers
  3. taq polymerase
  4. dNTPs
  5. buffers and salts
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3
Q

what enzyme is used in PCR to aid with replication

A

Taq polymerase

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4
Q

what are the steps in the PCR process (7)

A
  1. start with one double stranded DNA - initialisation
  2. denaturation
  3. the primers hybridise
  4. annealing
  5. extension - end with 2 double stranded DNA strands that are genetically the same
  6. repeat = cycling
  7. final extension and hold
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5
Q

what temp is normally required to denature a double stranded template DNA

A

94-98 degrees - a high temp to break the hydrogen bonds so the strands can separate

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6
Q

what temp range is required to hybridise the primers

A

50 - 64 degrees

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7
Q

what temp is required for elongation and what enzyme is involved at this step

A

72 degrees

DNA polymerase builds 5’ to 3’ taking nucleotides from the surrounding solution

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8
Q

how many PCR repeats equates to 1 billion copies of DNA

A

30

generally 30-32 cycles are used in PCR

2^30 =1 billion

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9
Q

what are the two biggest commercial uses of PCR

A

familial relationship testing

forensic investigation

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10
Q

what are 6 things we can do using PCR

A

look at hereditary diseases
use for gene expression
identify genes quickly
identify microbes or viruses
paleobiology
site directed mutagenesis

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11
Q

why is pure DNA not crucial for PCR

A

PCR allows for selective amplification due to the use of primers to show polymerase where to begin replication

so purity of the DNA isn’t crucial but it helps

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12
Q

why may only a pg amount of DNA be an issue in PCR

A

at pg level there may be interference of background levels/noise from instrumentation therefore ng is preferred if possible

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13
Q

what do primers do in PCR

A

primers are designed to attach to the edge of areas on DNA called STRs (Short tandem repeats) as the length of these are highly variable in humans

we analyse enough STR regions on the DNA to be able to get a profile representative of the individual

these primers signal to DNA polymerase where to start and stop replicating as polymerase can only add bases onto a pre existing strand

we have a stop and start primer for each STR regions considered

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14
Q

how are primers made for PCR

what does this process allow

A

primers can be synthesised using solid-phase phosphoramidite chemistry

this allows us to control what regions on the DNA are amplified and design/modify the primers to fit our needs

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15
Q

how many bases long are primers used in PCR

A

tend to be 15-30 bases long

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16
Q

why does the synthesised primer sequence need to be carefully designed

A

to ensure they bind properly to the correct region on the template DNA strand

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17
Q

what part of the PCR process do analysts have the most control over

A

the primer designed and therefore what regions of the DNA are being targeted

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18
Q

what does the primer concentration in the reaction mixture determine

A

the maximum yield of the intended product

the more primers the more likely they are to attach to the DNA

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19
Q

why is Taq polymerase used in PCR (2 reasons)

A
  1. this is the heat resistant form of polymerase enzyme - this enzyme is stable at 90 degrees or greater for short periods of time (minutes), other forms would denature (so stable to be used here)
  2. this enzyme works quickly - can replicate a 1000 base pair strand in under 10s
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20
Q

what is the source of taq polymerase

A

thermus aquaticus - a bacterium that lives in hot temps

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21
Q

what are dNTPs and what are they used for in PCR

A

dNTPs = deoxynucleoside 5’-triphosphates

these are the building blocks of the new DNA - building onto the 3’ end of the previous one

22
Q

how many dNTPs are there and what are they called

A

4
dATP
dCTP
dGTP
dTTP

23
Q

how much of each dNTP is added to the PCR reaction mixture

A

200 microM

24
Q

what is the purpose of the buffer and salts in the PCR reaction mixture

A

needed for the stabilisation of the hybridisation and extension processes

the strands are likely to denature without these present

salts - prevent electrostatic repulsion of phosphates
buffers - maintain stable pH

25
Q

what is meant by hybridisation in DNA

A

the process where two complementary single stranded DNA bond to become a double stranded molecule

26
Q

give an example of a buffer and a salt to be added to a PCR reaction mixture

A

tris-HCl = buffer

salt = MgCl2 (magnesium chloride)

27
Q

what happens in the initialisation stage of PCR

what is the temp and time normally here

A

ensure the template DNA is suspended in solution and begins to denature

some ‘hot start’ polymerases are activated here

94-96 degrees for 5 min

28
Q

when is the initialisation stage particularly important

A

when we have a very long template DNA strand

longer strands may need higher temps or longer initialisation times

29
Q

what happens in the denaturation stage of PCR

what temp and time are used here

A

the double stranded template DNA is split into two single strands

94-98 degrees for 30 secs

30
Q

what happens in the annealing stage of PCR

what temp and time are used here

what does the temp need to be lower than

A

primers bind to template strand
polymerase binds but doesn’t proceed

50-64 degrees for 30 secs

a few degrees lower than the melting temperature of the primers

31
Q

what happens in the extension stage of PCR

what temp and time are used here

A

the complimentary strand is synthesised via base pairing - the temp is optimised for the activity of the enzyme

72 degrees for 30 sec - or 1 min per 1000 bases on template

32
Q

what happens in the cycling stage of PCR

A

the denaturation, annealing and extension are repeated

can be anywhere between 15-40 repeats

every cycle doubles the conc of DNA

33
Q

what can too many PCR cycles lead to

A

limited dNTP concertation in solution so the strand is not synthesised correctly

can lead to truncated products = partial fragments of the intended products

34
Q

what can too few PCR cycles lead to

A

not enough amplification has occurred so the regions you want to analyse may not be able to be analysed

35
Q

what happens in the final extension stage of PCR

what temp and time are used here

A

ensures all the strands have finished being replicated and reduce the risk of having truncated products

72 degrees for a few minutes

36
Q

what happens in the final hold stage of PCR

what temp and time are used here

A

best storage condition for the PCR products

4 degrees until you use the products in electrophoresis

37
Q

what do the primers define in PCR

A

the length of the STR region being amplified

38
Q

how do PCR instruments work

A

Eppendorf sample tubes are places into the instrument

can do multiple samples at once

then programme the temperature sequence to what you need

39
Q

what is a common problem seen in PCR and what causes this issue (2 reasons)

A

the formation of primer dimers

due to the poor choice of the primer sequence or if too high a conc of primer is added

40
Q

what is a primer dimer

A

where two primers join to each other rather than onto the template DNA

41
Q

when do primer dimers become more of a problem

A

when looking at multiplexes - analysing more than 1 STR region at once

this is often the case for multiplexes nowadays

42
Q

give three other problems that may be seen in PCR (briefly explain why each may occur)

1 = 5 reasons
2 = 2 reasons
3 = 3 reasons

A
  1. no amplification of the DNA
    - too high primer conc
    - dNTPs degraded by freezing
    - degraded template strand
    - annealing temp too high
    - human error - forgot to add something to reaction mix
  2. non-specific amplification of the DNA
    - contamination
    - annealing temp too high
  3. weak amplification of the DNA
    - DNA conc too low
    - not enough PCR cycles
    - annealing time too short
43
Q

what is RNA used for and how can it be used in DNA replication

A

DNA give info on what cell is capable of whereas RNA gives info on what the cell is doing and builds proteins we use

we ca do reverse transcription to get DNA sequences from RNA ones:
- primers can be designed to bind to the RNA,
- synthesise the DNA strand from this
- denature from the RNA strand and then go on to be used in PCR

normally used in biosciences not forensics

44
Q

what is qPCR

A

quantitative PCR

a method that measures the concentration of the DNA product

used to track the process of the PCR cycles

45
Q

how is the concentration of DNA products measured in qPCR

A

the conc is proportional to the fluorescence signal

detects the fluorescence in real time

46
Q

how do DNA molecules being replicated on PCR show fluorescence for it to be detected in qPCR

A

a probe is attached to the template DNA strand

the probe has a fluorophore and a quencher attached to it

the quencher turns off the fluorescence, as polymerase goes along the template strand when it reaches the probe it digests it so the fluroescence is released into the solution and will now give a signal

47
Q

what does qPCR allow

A

the progress of the reaction to be tracked so any problems in amplification can be identified early on so we don’t waste time do all the cycles to realise it didn’t work

48
Q

in qPCR how many PCR cycles does it take for us to see a plateau in the DNA product concentration

why is this plateau seen

A

30-40 cycles - never do more than 40

due to running out of dNTPs to synthesise new strands or other components in the reaction mixture e.g primers

49
Q

what 6 components would be added to the PCR reaction mix to develop the covid vaccine

A

as vaccines use RNA the reaction mix is different to that used in DNA analysis of crime scene samples

reverse transcriptase
dNTPs
primers - these picked to highlight regions we want
taq polymerase
probe strands

50
Q

what is dPCR

A

digital PCR

scales up qPCR over multiple wells - qPCR = normally 1 sample at a time

use multiple wells and then count how many show amplification

51
Q

why might dPCR be used

A

more sensitive than qPCR and more precise measurement of DNA concentration

DNA (16 decks)

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