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finals 15% Flashcards

1
Q

⎯ most abundant macromolecules in biological
system

A

PROTEINS

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2
Q

⎯ measurable substance in the blood whose
presence is indicative of diseases or
environmental exposure

A

BIO MARKERS

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3
Q

Most common method for purifying proteins

A

COLUMN CHROMATOGRAPHY

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4
Q

Involves the separation of soluble components in a
solution by specific differences in physical-
chemical characteristics of the different constituents.

A

column chromatography

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5
Q

Contains a resin bearing either positively or negatively charged chemical group

A

ion exchange chromatography

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6
Q

Resins with positively charged group

A

Anion exchange resins

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7
Q

Uses the lock and key binding

A

affinity chromatography

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8
Q

Uses the principle that the protein binds to a
molecule for which it has specific affinity

A

affinity chromatography

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9
Q

⎯ Specific affinity where the protein binds to
carry out their biological activity

A

Ligand

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10
Q

Used for separation to determine the sizes and
presence or amount of DNA

A

electrophoresis

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11
Q
  • Anionic detergent (-)
  • Disrupt the structure of protein to be linear
    and binds most protein
A

SDS-PAGE

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12
Q

SDS coats all the polypeptides with negative charges

true or false

A

tru :»>

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13
Q

SDS electrophorese according to their ??

A

molecular masses

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14
Q

The electrophoretic mobility of proteins upon SDS page is
inversely proportional to the ?

A

molecular weight

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15
Q

organic dye which is most frequently employed method for protein detection in SDS page gel

A

coomassie blue staining

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16
Q

Advantages of?
o Quantitative binding of dye to
proteins
o Low price and good reproducibility

A

coomassie blue staining

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17
Q
  • Uses imidazole and zinc salt proteins for
    protein detection in electrophoresis gels
  • It is based on the precipitation of the zinc
    imidazole in the gel
A

ZINC-REVERSE STAINING

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18
Q

This technique is:
o Rapid
o Simple
o Cheap
o Reproducible
o Compatible with Mass
Spectrophotometer (MS) Analysis

A

ZINC-REVERSE STAINING

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19
Q

Based on the binding of silver ions in the
protein followed by reduction to free silver
sensation and enhancement

A

SILVER STAINING

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20
Q

Widely used because the sensitivity is below 1 nanogram per spot

A

SILVER STAINING

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21
Q

⎯ most popular and well-established
techniques for global protein separation and
quantification

A

GEL PROTEOMICS

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22
Q

⎯ the pH at which protein has no net charge paraneutral (no negative and no positively charge)

A

Isoelectric point

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23
Q

a laboratory method used to detect specific protein molecules from among a mixture of
proteins.

A

WESTERN BLOT

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24
Q

In western blot, the separated proteins are then transferred (blotted) to ?

A

nitrocellulose or nylon sheet.

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25
Q

Also known as electro transfer where the protein is
driven by an electrical field

A

electroblotting

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26
Q

⎯ provides a higher sensitivity than the color production system

A

Chemiluminescent

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27
Q

the enzyme activates a substrate or alkaline phosphatase and cyclic diacyl hydrazide for HR horseradish peroxidase

A

chemiluminescent

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28
Q

▪ we can use spectrophotometer for detecting proteins
▪ the amino acid with aromatic rings like tryptophan, tyrosine, and phenylalanine absorb UV wavelength

A

UV ABSORBTION METHOF

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29
Q

In here the peptide bonds of protein react with cupric
ions present in the biuret reagents under alkaline
conditions

A

BIURET METHOD

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30
Q

If cupric ions reacted in biuret agents it would produce
a _____color

A

purple

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31
Q

➢ This is a two-step reaction
➢ Same with biuret method ⎯ Cupric ions bind

A

LOWRY METHOD

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32
Q

In lowry, the only difference is that there is an addition
of ____________ reagent that is reduced to
increase the sensitivity

A

Folin-Ciocalteu

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33
Q

➢ It uses a similar principle that describes a violent
reaction

A

BICINCHONIC ACID METHOD

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34
Q

ELISA was introduced by___________ and
Peter Perlman in Stockholm university in Sweden

A

Eva Engvall

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35
Q

A common laboratory technique which is used to
measure the concentration of an analyte in a
solution

A

ELISA

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36
Q

a Quantitative immunological procedure in
which antigen antibody reaction

A

ELISA

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37
Q

➢ It uses a primary labeled antibody that react directly with the antigen
➢ It can be performed with the antigen that is directly immobilized on assay plate

A

DIRECT ELISA

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38
Q

➢ It utilizes a primary unlabeled antibody in
conjunction with a labeled secondary antibody
➢ Secondary antibody has a specificity for
primary antibody

A

INDIRECT ELISA

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39
Q

➢ Antigens like Tumor markers, hormones, serum
proteins may be determined
➢ Antigens in the sample bind with the capture antibody
and become immobilized

A

SANDWHICH ELISA

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40
Q

➢ Used to determine the precise mass of peptides.

A

Matrix-Assisted Laser Desorption Ionization-Time-
of-Flight (MALDI-TOF) spectrometry

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41
Q

very sensitive and accurate for
determining amino acid sequences

A

MALDI-TOF

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42
Q
  • Amount of protein that can be produced for
    each sample or amount of proteins that can
    be detected for each sample
A

Throughput

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43
Q

The extent to which two
sequences are the same.

A

IDENTITY

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44
Q

Lining up two or more sequences to search for the
maximal regions of identity in order to assess the extent of
biological relatedness of homology.

A

ALIGNMENT

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45
Q

A fixed set of commands in a computer program

A

ALGORITHM

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46
Q

A space introduced in alignment to compensate for
insertions or deletions in one of the sequences being
compared

A

GAP

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47
Q

The sequence presented for comparison with all other
sequences in a selected database

A

QUERY

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48
Q

Study on evolutionary relatedness among species
by comparing homologies and differences in gene
sequences

A

PHYLOGENETICS

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49
Q

➢ A field which uses computers to store and analyze
molecular biological information
➢ It is about finding and interpreting biological data
online

A

BIOINFORMATICS

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50
Q

o Study of all RNA molecules in a living organism

A

TRANSCRIPTOMICS

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51
Q

o pertains to microbes (fungi,
parasites, viruses and bacteria); the
genomes of these organisms are
described within a specific
environmental like niche or location

A

MICROBIOMICS

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52
Q

o involves description of chemical
processes involving metabolites

A

METABOLOMICS

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53
Q

o description of the entire complement of proteins in a living organism
o study the sequence and all the properties of proteins

A

PROTEOMICS

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54
Q

 Composed of a group nucleotide sequence
entity
 Data repositories that accept nucleic acid
sequences data and make it freely available in
the public,

A

Nucleic Acids (International Nucleotide Sequence
Database)

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55
Q

⎯ Biological database that collects
DNA sequences
⎯ Located at the National institute of
genetics in the Shisuka

A

DDBJ (DNA Databank of Japan)

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56
Q

⎯ A nucleic acid database that comes under European bioinformatics institute, which was also established in collaboration with the DDBJ and GenBank

A

EMBL (European Molecular Biology Lab)

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57
Q

⎯ It is the genetic sequence database
⎯ Placed the collected publicly
available DNA sequences

A

GENBANK

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58
Q
  • links scientists to bioinformatics solutions
    by collaborations, data, and software
    development
A

National Center for Genome Resources
(www.ncgr.org/)

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59
Q
  • stores and archives DNA sequences from
    both large-scale genome projects and
    individual laboratories
A

Genbank (www.ncbi.nlm.nih.gov/Genbank)

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60
Q
  • gene sequence collection containing data on
    map location of genes in chromosomes
A

Unigene (www.ncbi.nlm.nih.gov/UniGene)

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61
Q
  • Centre for research and services in
    bioinformatics; manages databases of
    biological data
A

European Bioinformatic Institute (www.ebi.ac.uk)

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62
Q
  • automatic annotation database on
    genomes
A

Ensembl (www.ensembl.org)

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63
Q

➢ Contain original data in the form of primary
sequence data or structural data as submitted by the
scientific community.

A

PRIMARY DATABASES

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64
Q

➢ Collects and present data after comparing and filtering
them from different primary databases and exhibit
only the non-redundant sequences

A

COMPOSITE DATABASES

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65
Q

➢ Contain information that has been process and
derived from the raw data available in primary
database
➢ Derived from the results of analyzed primary data

A

SECONDARY DATABASES

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66
Q

the NIH genetic sequence database, an
annotated collection of all publicly available DNA
sequences

A

GENBANK

67
Q

o identifier for the sequence that

A

Accession number

68
Q

o number assigned to this sequence
when it was submitted to GenBank
o when identifier is used, we need to
search for a specific sequence

A

GI (gene Identification)

69
Q
  • the main databases used for the
    prediction of the 3D structures of proteins
    and nucleic acid
A

PROTEIN DATA BANK

70
Q
  • is called the PDB ID or identifier
  • Crystal structure of sickle cell or
    sickle hemoglobin
A

5E6E

71
Q

➢ A way of rearranging sequences of DNA, RNA or
protein to identify regions of similarity.

A

SEQUENCE ALIGNMENT

72
Q
  • Compare two sequences
    o EMBOSS WATER
    o BLAST
A

PAIRWISE

73
Q

Compare more than two sequences
o MUSCLE
o MAFFT
o CLUSTAL Omega

A

MULTIPLE

74
Q

⎯ matching the residues (bases or amino acids)
of two sequences across their entire length

A

GLOBAL ALIGNMENT

75
Q

o indicates identity meaning they are the same

A

Straight line

76
Q

➢ matching of two sequences from regions which
have more similarity with each other
➢ The two sequences may or may not be related
➢ ONLY A PORTION WILL ALIGN

A

LOCAL ALIGNMENT

77
Q

Denotes purines
* Guanine or adenine

A

R

78
Q

This program creates a multiple sequence alignment
using the DNA or protein sequence of the
organisms

A

CLUSTAL OMEGA

79
Q

➢ finds regions of local similarity between sequences.
➢ the amino acid sequences of proteins or the
nucleotides of DNA sequences.

A

BLAST

80
Q

o when you are aligning nucleotide
to nucleotide

A

Blastn

81
Q

For novel DNA sequences and EST analysis

A

BLASTx (protein database)

82
Q

For STS and EST assignment in databases

A

TBLASTx (nucleotide translated database)

83
Q
  • Find proteins highly similar to your query
A

SmartBLAST

84
Q
  • Design primers specific to your PCR
    template
A

Primer-BLAST

85
Q
  • Search immunoglobulins and IT cell receptor
    sequences
A

IgBLAST

86
Q
  • Establish taxonomy for uncultured
    environmental sequences
A

MOLE-BLAST

87
Q

Molecular techniques are also referred to as

A

GENOTYPE ASSAYS/ TESTING

88
Q

⎯ routine way of identifying microorganisms or
we base it in the phenotype of an organism

A

PHENOTYPE / PHENOTYPING ANALYSIS

89
Q

focuses more on the
physiological properties of microorganisms

A

Phenotype

90
Q

majority of microorganisms will grow after___hours
and some 48 hours

A

24 hrs

91
Q

denotes the presence or growth of a bacterium/
bacteria (pathogen)

A

COLONIES

92
Q

 common for bacterial sample
 16S rRNA or 23S rRNA

A

BACTERIA (16S rRNA or 23S
rRNA)

93
Q

 common target for fungi
 18S rRNA

A

FUNGI (18S rRNA)

94
Q

When we perform or do different sequencing assays,
the most common sequencing test is under the?

A
  • NGS (Next Generation Sequencing
    techniques)
95
Q

the commonly sequence gene is the ?

A

16S rRNA

96
Q

it contains the SIGNATURE SEQUENCE which makes an
organism UNIQUE

A

conserved region

97
Q

➢ Also, an arthropod borne ⎯ it is also an infection
acquired via blood sucking insects

A

BORRELIA SPECIES

98
Q

o refers to your bacteria that has a
spiral shape

A

Spirochetes

99
Q
  • Highest valuable diagnostic approach in
    acute ill patients (borrelia species)
A

PCR

100
Q
  • one of the most recently applied
    techniques possible for detecting borrelia
    specie
A

NEXT GENERATION SEQUENCING and
PROTEOMIC APPROACHES

101
Q

➢ This bacterium, it is an important cause of a sexually
transmitted disease, especially in the United States

A

CHLAMYDIA TRACHOMATIS

102
Q

➢ Another organism which is also very difficult to grow
using our classical methods because it is considered to be an Anaerobic
microorganism

A

CHLOSTRIDIUM DIFFICILAE

103
Q

➢ Another name of infection is, ANTIBIOTIC
ASSOCIATED BACTERIA
➢ Mainly responsible for hospital acquired bacteria
➢ This bacteria is only PATHOGENIC

A

chlostridium difficilae

104
Q

another commonly used method; one-step,
rapid, and specific screening method for
Chlostridium difficilae toxin genes

A

multiplex pcr

105
Q

➢ a bacterium which is commonly missed out; cannot
be easily identified

A

MYCOPLASMA PNEUMONIAE

106
Q

THE ONLY BACTERIA which DO NOT
HAVE CELL WALL

A

mycoplasma pneumoniae

107
Q

⎯ refers to the blackening
in the area of infected site

A

Eschar

108
Q

How do we diagnosed Rickettsia using Molecular
Techniques?

A

➢ PCR BASED ASSAYS

109
Q

➢ the most common isolates in the laboratory

A

STAPHYLOCOCCUS AUREUS

110
Q
  • This is a specific strain of the Staph. A
  • This strain is mainly because of a mutation
    of the gene MecA and MecB gene of your
    S.A
A

MRSA
(Methicillin Resistant Staphylococcus aureus)

111
Q

Best molecular diagnostic tool for MRSA
detection

A

pcr

112
Q
  • latest development in the direct MRSA
    detection and identification; much better
    technique
A

Real-Time PCR Assay

113
Q

➢ Is also a causative agent of pneumonia
➢ Streptococcus’ genus is strained or identified under
the microscope

A

STREPTOCOCCUS PNEUMONIAE

114
Q

➢ is like a counterpart of Streptococcus
➢ also termed as GAS (Group A Streptococcus)

A

STREPTOCOCCUS PYOGENES

115
Q

➢ Also known as GBS (Group B Streptococcus)
* clinically significant for the Neonates
(newborn)

A

STREPTOCOCCUS AGALACTIAE

116
Q

⎯ Rapid detection of GBS

A

Conventional and real-time PCR assays

117
Q

How do we detect Aspergillus through molecular
techniques?

A
  • NUCLEIC ACID AMPLIFICATION
    TECHNIQUES (NAAT)
118
Q

➢ This virus belongs to the family of Retroviridae
specifically under the genus: Lentivirus

A

HUMAN IMMUNODEFICIENCY VIRUS

119
Q

o Global
o this type is also considered to be the most virulent
o occurs globally, main focus

A

HIV 1

120
Q

Codes for CORE STRUCTURAL CHON

A

Gag

121
Q

Binds to CD4 receptors

A

env

122
Q

one of the commonly used confirmatory methods for HIV
detection

A

Western blot

123
Q

➢ Focuses or contains lots of strains which cause
different and wide varying types of infection

A

HUMAN PAPILLOMAVIRUS

124
Q

➢ Composed of different types of viruses
➢ More than 1 virus → means you have different
classes and different families of viruses

A

HEPATITIS VIRUSES

125
Q

Among all the molecular techniques for Hepatitis
virus, one of the most widely used assay is the

A
  • Quantitative PCR assays
126
Q

➢ which is an emerging technique (new technique)
used for identification of genus and species of your
microorganism, specifically your bacteria

A

MALDI-TOF MS

127
Q

what is mainlythe principle of MALDI-TOF MS?

A
  • SOFT IONIZATION
128
Q

How will you purify your proteins?

A
  • by mixing a specific reagent
129
Q

o refers to the complete set of chromosomes in the cells of the organism,

A

Karyotyping

130
Q

it used radiolabeled probes as the target
label

A

IN SITU HYBRIDIZATION

131
Q
  • this is a tagging technique or a method on
    how we add the probe into the sample or
    reagent
A

NICK TRANSLATION

132
Q

not metaphase stage of mitosis is changed but
instead the one being changed is the INTERPHASE
STAGE

A

INTERPHASE FISH

133
Q

➢ in this pattern or in this application, you use
different types of probes
➢ you use different many probes from a single
chromosome

A

WCP (WHOLE CHROMOSOME PAINTING

134
Q

PRINCIPLE:
* on those chromosomes or single
chromosome, there are lots of unique
DNA associated with it

A

WCP

135
Q

➢ much more automated because it uses a
computer assisted system
➢ It has a program/system/software installed
wherein the main profile is already uploaded,

A

MFISH - MULTICOLOR-FISH

136
Q

You will be able to observe multiple
chromosomal aberrations or changes

A

SKY

137
Q

the probe is a telomere probe which will recognize 6
base repeats
➢ It detects the SIX BASE REPEATS SEQUENCE
which is present at the ends of all chromosomes

A

ALL-TELOMERE-FISH

138
Q

➢ You simply compare the DNA content of
differentially labelled normal from abnormal cell
population

A

COMPARATIVE GENOMIC HYBRIDIZATION

139
Q

was introduced in the
late 1800s despite much skepticism.

A

FINGERPRINTS

140
Q

the highest amount of DNA in male is
the

A

→ SEMEN

141
Q
  • must be plucked for more DNA sample
    (directly from hair root with little tissue
    obtained)
A

HAIR SAMPLES

141
Q
  • must be plucked for more DNA sample
    (directly from hair root with little tissue
    obtained)
A

HAIR SAMPLES

142
Q
  • one of which has lowest concentration of
    DNA sample
A

URINE

143
Q

o short sequences of bases that
repeats many times
o this is the portion gene

A

SHORT TANDEM REPEATS (STRs

144
Q
  • This acts as fillers or spacers between of
    that coding portions of the chromosome
A

SATELLITE DNA

145
Q

if it has 2 – 5 repeats
* it is termed as

A

MICROSATELLITE DNA

146
Q

If it has 9 – 10 repeats
* it can now be termed as

A

MINI-SATELLITE

147
Q

A short nucleotide sequence that is paired with one
strand of DNA and provides a free 3’-OH end

A

PRIMER

148
Q

➢ A single sequence used for the amplification of a
similar gene related to a specific genus

A

UNIVERSAL PRIMER

149
Q

➢ can anneal only to the templates from one species
➢ used when the DNA sequence is KNOWN
➢ amplifies only the intended target

A

TARGET-SPECIFIC PRIMER

150
Q

the midpoint of temperature range over which
the DNA is denatured.

A

MELTING TEMP

151
Q

The annealing temperature should be __°C lower than
the Tm

A

5

152
Q

The recommended GC is about

A

50%

153
Q

optimum melting temperature

A
  • 52-58°C
154
Q
  • It attached on others and not on the target
A

Mispriming

155
Q
  • One of the most expensive tests in the
    laboratory
A

Molecular Testing

156
Q

o is a process of removing calcium
in the tissue,
o it reduces DNA and RNA recovery

A

Decalcification

157
Q

OD 260/280 ratio of 1.8 to 2.0
 sample is ??

A

pure

158
Q

Store extracted DNA and RNA samples, clearly
labeled, at __°C or lower

A

20

159
Q

Store PCR products in a separate freezer at __°C
or lower

A

20

160
Q
  • Is used almost exclusively for quality
    control in sequencing projects
  • it can be used to investigate fragment size
    distribution and final library quality
    assessment.
A

CAPILLARY GEL ELECTROPHORESIS

161
Q

➢ Also known as proficiency testing (PT),
* is inevitable for monitoring performance.
➢ It is necessary to periodically assess the analytical
performance of molecular tests

A

EXTERNAL QUALITY ASSURANCE (EQA)

162
Q

➢ Is necessary to ensure high assay reproducibility
and performance,

A

INTERNAL QUALITY ASSURANCE (IQA)

molbio (3 decks)

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