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Molecular Biology > Module 6: Detection and Analysis of Nucleic Acid > Flashcards

Module 6: Detection and Analysis of Nucleic Acid Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Macromolecules that exists as polymers
called polynucleotides.

A

Nucleic acid

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2
Q

Formation of a nucleotide by adding ____ group to a nucleoside

A

phosphate groups

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3
Q

phenol and chloroform/isoamyl alcohol
(25:24:1) are mixed with an equal
volume of samples by vortexing

A

Organic purification

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4
Q

involves the incubation of nuclei with only proteinase K at 65°C

A

Inorganic Purification

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5
Q

movement of DNA or RNA in response to an electric field

A

Electrophoresis Separation

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6
Q

DNA are reduced to fragments by digestion with ____.

A

restriction enzymes

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7
Q

are small molecules and no digestion is required prior to electrophoresis.

A

RNA

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8
Q

Routinely uses Gel electrophoresis.
Uses TAE or TBE.

A

Molecular separation of DNA

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9
Q

interaction between single stranded nucleic acid to form a (duplex) double stranded molecules based on complementary base
pairing of the sequences.

A

Nucleic Acid Hybridization

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10
Q

process of recombination of two non-labeled strands into a stable double stranded structure.

A

annealing

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11
Q

If one strand has a marker, a hybrid is formed between labeled and an unlabeled strand.

A

hybridization

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12
Q

labeled strand is called the ____ and the product is called ____

A

probe; hybrid

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13
Q

sample and probe in a solution

A

Liquid or Solution Phase Hybridization

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14
Q

e.g. Digene Hybrid-Capture 2, Digene Corp. USA

A

Liquid/Solution Phase Hybridization

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15
Q

Hybridization assay formats for detection of HPV

A

Liquid or Solution Phase

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16
Q

occurs in biphasic environment

A

Solid Support Hybridization

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17
Q

solid phase in solid support hybridization

A

sample

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18
Q

liquid phase in solid support hybridization

A

probe

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19
Q

e.g. dot or blot

A

Solid Support Hybridization

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20
Q

What are the two Hybridization assay formats

A

Liquid or Solution Phase Hybridization
Solid Support Hybridization

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21
Q

described by E.M. Southern in 1975, detect specific DNA sequences and gene mutations

A

Southern Blot

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22
Q

Blotting techniques in which examples are electrophoretic separation, transferring to solid support nitrocellulose and hybridization

A

Southern blot

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23
Q

Blotting technique that uses RNA sample

A

Northern Blot

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24
Q

RNA is extacted, digested, electrophoresed, blotted and probed.

not routinely used in clin lab because RNA is not stable

A

Northern blot

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25
Q

in northern blot technique, how many minutes and in what temp is rna denatured?

A

15 min of 55 C heating

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26
Q

used to identify proteins
separated by PAGE

A

Western Blot

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27
Q

confirmatory for HIV and used in the diagnosis of Lyme Disease

A

Western blot

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28
Q

membranes used in western blotting

A
  • nitrocellulose
  • nylon
  • PVDF or Polyvinylidene difluoride
29
Q

probe molecule in southern and northern blotting

A

DNA

30
Q

western blotting probe molecule

A

antibody

31
Q

south-western blotting probe molecule

A

dsDNA

32
Q

Results from a variable number of tandem repeats (VNTR) in a short DNA FRAGMENT.

used in FORENSIC DIAGNOSIS, DONOR TRANSPLANTS.

A

RESTRICTION FRAGMENT LENGTH POLYMORPHISM

33
Q

In RFLP, restriction fragments are separated on gel and analyzed by ____ blotting techniques.

A

southern

34
Q

*amplified nucleic acids, whether an RNA or DNA are referred to as

A

amplicons

35
Q

patented the PCR method in 1985

A

Kary Mullis

36
Q

target amplification method if the nucleic acid of interest is RNA rather than DNA, conversion of RNA to DNA

A

reverse-transcriptase PCR

37
Q

TA method which uses numerous primers for different targets in the same mixture

A

Multiplex PCR

38
Q

target amplificationa nd detection steps occur simultaneously and PCR product is detected using fluoresent dyes

A

Real-Time PCR

39
Q

uses probes or pieces of DNA or RNA that are labelled with a detectable molecule, such as biotin, dyes, or radioactive isotopes. These probes bind complementary to the target.

A

Probe Amplification Methods

40
Q

examples of probe amplification methods

A

ligase chain reaction, cycling probe technology, cleavase invader

41
Q

what are examples of amplification methods

A

target amplification
probe amplification
signal amplification

42
Q

Relies on specific recognition and cleavage of particular DNA
structures by flap endonuclease-I family of DNA polymerases

A

Cleavase/Invader Technology

43
Q

two primers are designed that hybridize target sequence in an
overlapping manner.

A

Cleavase/ Invader Technology

44
Q

uses a stimuli to generate a signal, where the signal is proportional to the amount of the target sequence present in the clinical specimen assays

A

Signal Amplification Methods

45
Q

examples are Branched DNA and Hybrid capture Assay

A

Signal amplification methods

46
Q

a fully automated method, dsDNA is target of exponential amplification, amplifies target nucleic acid without use of thermocycler

A

Strand displacement amplification

47
Q

an isothermal assay, targets either DNA or RNA ;
RNA is the amplified product, detection of M. tuberculosis

A

TMA or Transcription Mediate Amplification

48
Q

similar to TMA but only RNA is targeted for amplification;
detection of HIV and CMV

A

NASBA or Nucleic Acid Sequence-Based Amplification

49
Q

uses a collection of spots attached to a solid support that is capable of quantitating hundreds or even thousands of genes in a cell or a tissue simultaneously

A

Microarray or DNA Chip technology

50
Q

separation of dsDNA to ssDNA and breaking of H bonds between base pairs

A

DENATURATION

51
Q

between individual nucleotides or phosphate backbone; breaks in the backbone of DNA molecule either dsDNA or ssDNA

A

DEGRADATION

52
Q

2 Causes of DNA Degradation

A
  1. Using very old DNA samples
  2. Using DNA extracted from formalin-fixed paraffin embedded samples
53
Q

short term storage in weeks for DNA sample

A

4 C in Tris-EDTA

54
Q

medium-term storage in months of DNA

A

-80 C in Tris-EDTA

55
Q

Long-term storage in years under ethanol of DNA

A

-80 C as a precipitate

56
Q

long term storage of DNA in decades

A

-164 C or dried

57
Q

steps to prevent DNA degradation

A
  • correct handling and storage
  • perform extractions at 40C on ice or in the cold
  • inhibit nuclease activity
  • store purified DNA correctly
58
Q

addition of phosphate groups is via

A

phosphoric anhydride linkage

59
Q

examples of methods to determine nucleic acid purity and yield

A
  • DNA Spectrophotometry
  • Nanodrop Spectrophotometry
  • Fluorometric Methods
  • Real-Time PCR
60
Q

Methods for Nucleic Acid Analyses

A
  • Electrophoresis
  • Hybridization Assay
  • DNA Sequencing
  • Polymorphism based
  • Amplification Techniques
61
Q

AGE means

A

Agarose Gel Electrophoresis

62
Q

PAGE

A

Polyacrylamide Gel Electrophoresis

63
Q

SDS-PAGE

A

Sodium dodecyl-sulfate Polyacrylamide gel Electrophoresis

64
Q

DGGE

A

Denaturing gradient gel electrophoresis (DGGE)

65
Q

TAE means

A

Tris-acetate-EDTA

66
Q

TBE

A

Tris-Borate-EDTA

67
Q

short nucleotide sequence complementary to a specific DNA sequence and initiate DNA replication

A

Primers

68
Q

provides a free 3’-OH for DNA polymerase to start synthesis of chain

A

primers

69
Q

use to target a particular sequence of complementary DNA or RNA ; can be labeled with radionuclide (P32), enzyme, and biotin

A

Probes

Molecular Biology (5 decks)

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