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Sensors > Structural sensing > Flashcards

Structural sensing Flashcards

1
Q

What do we mean by structural sensing?

A

detection of a threat by use of the structural elements of the threat, usually from binding to part of these elements with something that is easy to detect

eg an agglutination test

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2
Q

What are the five bio-analysis methods?

A

Culture
Microscopy
Immunoassay
PCR
Chemical Assays

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3
Q

Describe Method of Bioanalysis Culture

A

grow agents in conditions that specifically relate certain types of bacteria/fungi etc ie rose Bengal agar is a growing media that inhibits bacteria and allows the identification of the presence of yeast and moulds

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4
Q

Describe Method of Bioanalysis Microscopy

A

Morphological identification of particles

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5
Q

Describe Method of Bioanalysis Immunoassay

A

particles with specific epitopes matching the assay antibodies

particles with parts of the allergen that are identified by the body (epitodes) that in this case match the antibodies present in the assay test.

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6
Q

Describe Method of Bioanalysis PCR

A

DNA matching test

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7
Q

Describe Method of Bioanalysis chemical assays

A

identify the biomass of specific chemicals eg ATP

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8
Q

Limitations of bioanalysis method culture

A

underestimates concentration of all organisms
nonculturable organisms are invisible
non culturable are classed as noninfective

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9
Q

Limitations of bioanalysis method microscopy

A

limited to groups of organisms, not specific strains

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10
Q

Limitations of bioanalysis method immunoassay

A

limited to organisms that the assay is designed for, therefore only binary results
Cross reactivity is common

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11
Q

Limitations of bioanalysis method PCR

A

limited to organisms that the assay is designed for, therefore only binary results
highly specific
highly sensitive

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12
Q

Limitations of bioanalysis method Chemical analysis

A

only an indicator for large quantities of organisms

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13
Q

what is meant by direct binding event?

A

direct binding of the target to a specific molecular recognition element

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14
Q

how does direct binding event works?

A

a reversable ‘lock and key’ event like and antibody with a viral protein

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15
Q

9 molecular recognition elements for biosensing

A

single strand DNA
Antibody
Peptide
Enzyme
Lectine
Receptor
Aptamer
Small molecule
imprinted molecule

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16
Q

What is an antibody?

A

also known as an immunoglobulin Ig is a large, Y shaped protein produced mainly by plasma cells that is used by the immune system to neutralize pathogens such as pathogenic bacteria and viruses.

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17
Q

How do immunoassay ticket systems work?

A

liquid sample added to test strip and other reagents added if required

target molecules wick through the ticket, bind to immobilized agents and detection molecules in a ‘sandwich’ format

wick usually travels through a testing area before reaching a control line, if no line shows up on control after allotted time, then the test needs repeating.

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18
Q

Define SELEX?

A

Systematic Evolution of Ligands by EXponential Enrichment

a method of increasing the number of DNA/RNA strands required for testing and use them to sequence and characterise DNA found in the environment

The starting single stranded DNA or RNA library
(10 14 ~10 16 random oligonucleotides) is composed of sequences 20~100 nucleotides in length with a random region in the middle flanked by fixed primer sequences.

After incubation with the target of interest, the bound
oligonucleotides are partitioned from unbound
sequences and amplified by PCR . repeated 2-15 times before used as biomarker identification tools.

The resulting enriched DNA pool is used for the next round of selection.

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19
Q

What is SELEX short for?

A

Systematic Evolution of Ligands by EXponential Enrichment

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20
Q

Dog’s nose; how does this compare with current detection systems

A
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21
Q

6 high level approaches for structural sensing

A

Magnetic
optical
electrochemical
mass
acoustic/piezoelectric
MEMS

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22
Q

Types of optical

A

Fluorescence
Absorbance
SPR/RM
Luminescence
RAMAN

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23
Q

Types of magnetic

A

magneto-elastic
giant magneto-resistance (GMR)

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24
Q

types of MEMS

A

MEOMS
cantilevers
microfluids
microcalorimetry

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25
Q

types of acoustic/piezo-electric

A

surface wave acoustic
quartz microbalance

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26
Q

types of mass

A

time of flight ion trap
ion mobility (MS/MS)

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27
Q

types of electrochemical

A

amperometry
potentiometric
conductimetric
molecular electronics

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28
Q

What is a molecular recognition element?

A

Molecular recognition event is typically a specific interaction that is reversible, analogous to the interaction between a lock and a key, although in many cases the binding would more accurately be described as induced fit, during which the recognition element changes shape upon binding.

29
Q

What does a direct binding event rely on?

A

Affinity of the target for the molecular recognition elements
Non-specific binding of extraneous material at the binding site
Sensitivity of detection
If attomolar (10 18 ) detection levels are required then high affinity molecular recognition elements with minimal non specific binding required

30
Q

considerations for structure based sensing?

A

Sample collection,
Sample concentration,
Binding of the target to the molecular recognition element,
Possible addition and removal of “reporter” groups,
Detection of target molecular recognition element complex,
Analysis of the output signal,
Renewal of the sensor surface for repeated monitoring.

31
Q

target inhibitor for single strand DNA?

A

complementary sequence of DNA

32
Q

target inhibitor for Antibody

A

proteins, carbohydrates, small organic molecules etc

33
Q

target inhibitor for Peptide

A

proteins, carbohydrates, small organic molecules etc

34
Q

target inhibitor for enzyme

A

substrate such as biochemicals like glucose, acetic acid

35
Q

target inhibitor for lectin

A

carbohydrate

36
Q

target inhibitor for receptor

A

proteins, carbohydrates, small organic molecules

37
Q

target inhibitor for aptamer

A

proteins, carbohydrates, small organic molecules etc

38
Q

target inhibitor for small molecules

A

proteins, cells etc

39
Q

target inhibitor for imprinted moelcules

A

proteins, small organics molecules, whole cells etc

40
Q

target inhibitor for

A
41
Q

8 SELEX methods

A

IP-SELEX
Capture-SELEX
Cell-SELEX
CE-SELEX
M-SELEX
AFM-SELEX
AEGIS-SELEX
Animal-SELEX

42
Q

Key aspects of IP-SELEX

A

includes immunoprecipitation

43
Q

Key aspects of Capture-SELEX

A

oligonucleotide library is immobilized on a support instead of the targets to identify aptamers against small soluble molecules

44
Q

Key aspects of Call-SELEX

A

utilizes whole live cells as targets for selection of aptamers

45
Q

Key aspects of CE-SELEX

A

involes separation of ions based on electrophoretic mobility

46
Q

Key aspects of M-SELEX

A

combines SELEX with a microfluid system

47
Q

Key aspects of AFM-SELEX

A

employs AFM to create a 3D image of the sample surface

48
Q

Key aspects of AEGIS-SELEX

A

utilizes libraries with the artificially expanded genetic code

49
Q

Key aspects of animal-SELEX

A

aptamers are selected directly within live animal models

50
Q

advantages of IP-SELEX

A

selects aptamers against proteins under normal physiological conditions
increased affinity and specificity

51
Q

advantages of Capture-SELEX

A

suitable for the selection of aptamers against small molecules
immobilization of the target not required
used for discovery of structure switching aptamers

52
Q

advantages of Cell-SELEX

A

Prior knowledge of the target not required
Aptamers are selected against molecules in their native state
Many potential targets available on the cell surface
Protein purification not required

53
Q

advantages of CE-SELEX

A

Fast
only 1-4 rounds of selection required
reduced non specific binding
target immobilization not required

54
Q

advantages of M-SELEX

A

Rapid
Very effective (small amounts of reagents required)
Applicable to small molecules
Automatable

55
Q

advantages of AFM-SELEX

A

able to isolate high affinity aptamers
Fast 3-4 rounds

56
Q

advantages of AEGIS-SELEX

A

high specificity of the selected aptamers

57
Q

advantages of animal-SELEX

A

selected aptamers bind the targets in their natural environment
Prior knowledge of target not required
Minimal optimization needed

58
Q

advantages of -SELEX

A
59
Q

disadvantages of IP-SELEX

A

more time consuming than standard SELEX

60
Q

disadvantages of Capture-SELEX

A

some oligonucleotides from the library might not be released/selected

61
Q

disadvantages of Cell-SELEX

A

suitable for cell surface targets
Requires high level of technical expertise
Costly
Time consuming
Post SELEX identification of target required

62
Q

disadvantages of CE-SELEX

A

not suitable for small targets
expensive equipment

63
Q

disadvantages of M-SELEX

A

Not suitable low purity/recovery of aptamers
target immobilization required

64
Q

disadvantages of AFM-SELEX

A

expensive equipment required
Immobilization of target aptamers required

65
Q

disadvantages of AEGIS-SELEX

A

Poor recognition of the unnatural bases by natural DNA polymerases

66
Q

disadvantages of Animal-SELEX

A

time consuming (man rounds required)

67
Q

Dog’s nose; how does this compare with current detection systems?

A

test kits in the range of 1g-1ug (visible to particles)
Field instruments in the range of 1ug-1pg (particles/vapour)
Dogs in the range of 1fg-1ag (vapour)

68
Q

Dog density of olfactory epithelium?

A

170cm^2
(humans have 10cm^2)

69
Q

How does the dog receptors mean it has a better sense of smell?

A

It is the interactions of odour molecules with specific receptor proteins that give specificity.
Each olfactory odour receptor neuron has only one functional odour receptor; if the odour molecule interacts with the receptor then the nerve cell will respond.

Sensors (17 decks)

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