MolDx Flashcards
1
Q
What enzyme is involved in the DNA replication in prokaryotes?
A
DNA Polymerase III
2
Q
What are the 3 steps of DNA replication?
A
Initiation, elongation and termination
3
Q
What is the function of DNA helicase?
A
Unwind the DNA zipper to initiate replication
4
Q
During transcription, which enzyme unwind the DNA strands?
A
DNA Helicase
5
Q
In order for transcription to start, what factors are involved?
A
DNA helicase, RNA polymerase II, transcrption factors and histone modification enzymes
6
Q
Rho factor is
A
A helicase enzyme that associates with RNA pol and inactivates elongation complex at a cytosine-rich termination site in the DNA.
7
Q
Rho independent termination occurs at
A
A G:C-rich region in the DNA, followed by A:T-rich regions
8
Q
What enzyme catalyzes mRNA synthesis in eukaryotes
A
RNA Polymerase II
9
Q
RNA Polymerase III transcription termination requires
A
A termination factor
10
Q
In prokaryotes, which enzyme catalyzes the synthesis of all RNA
A
RNA Pol II
11
Q
Which enzyme synthesizes mRNA in eukaryotes
A
RNA Pol II
12
Q
Transcription takes place in the:
A
Nucleus
13
Q
rRNA is synthesized by
A
RNA Polymerase I
14
Q
In prokaryotes, the basal transcriptional complex comprises of
A
Large and small subunits of RNA pol II and aditional sigma factors
15
Q
During transcription, the first ribonucleoside triphosphate retains all of its phosphate group
A
True
16
Q
hnRNA stands for
A
Heterogeneous nuclear RNA
17
Q
In eukaryotes, transcription termination is activated when
A
mRNA reaches the polyadenylation signal (poly A site). Poly A tail is important for the mRNA stability and translation into protein.
18
Q
RNA pol I terminates transcription at
A
Sal box + termination factor, TTFI
19
Q
RNA pol III termination factor is
A
A run of adenine + termination factor
20
Q
Which one do not have operons? Eukaryotes or Prokaryotes
A
Eukaryotes
21
Q
The boundaries nucleotides located at the beginning and end of introns are:
A
GT - AG (GT AG rule)
22
Q
TATA box is
A
A stretch of T and A nucleotides located aprox. 25 upstream of the transcription start site that signals the start of transcription
23
Q
RNA splicing refers to
A
The removal of the intronic sequences
24
Q
A key step in the transcription initiation by RNA polymerase II is
A
The phosphorylation of the RNA pol II tail, called CTD (C terninal domain)
25
RNA pol I and III lack
CTD domain. They have a CBC (Cap-binding complex) domain, which helps the RNA to be processed and exported.
26
UAA, UAG and UGA are nucleotides that signal
STOP codons
27
Translation initiation codon, also known as START codon is
AUG the first methionine (in eukaryotes).
28
The preferred consensus recognition sequence for translation to start in eukaryotes is
5'-ACCAUGG-3'
29
Bacteria mRNA are often referred as polycistronic, which means
The same mRNA encodes several different proteins, each translated from the same mRNA
30
DNA has a
Sugar-phophate backbone.
31
Denaturing reagents (formamide, urea) displace hydrogen bonds and separate the 2 DNA strands
True
32
DNA replication proceedes in a continuous way in which strand?
3' to 5' strand or leading strand
33
Okazaki fragments are
Small discontinuous fragments generated during the replication of the lagging strand (5' to 3'), which is copied in a discontinuous way.
34
DNA polymerase III is the main polymerizing enzyme during bacterial replication
True
35
DNA pol III holoenzyme complex is prokaryotes is required for
Priming, initiation, regulation and termination of the replication process
36
3' 5' exonuclease activity function is to proofread the replIcating DNA strand
True
37
The function of the poly A tail is
To activate the termination of the transcription
38
How do purines and pyrimidines differ?
Purines (adenine and guanine) are two-carbon nitrogen ring bases while pyrimidines (cytosine and thymine) are one-carbon nitrogen ring bases.
39
What is DNA primase?
DNA primase is an enzyme involved in the replication of DNA. Its function is to synthesize small RNA primers
40
What are the purpose of nucleic acid extraction?
To release the nucleic acid from cells and use in subsequent procedures
41
What are the three ways used to break though bacterial and fungi cell walls?
Mechanical (glass beads or grinding), enzymatic and a combination of detergent, strong base, Tris base, EDTA and glucose.
42
DNA extracted by boiling or alkaline (strong base as (NAOH) is denatured (single strand). Because of that, this DNA cannot be used for some applications that require double strand DNA such as restriction analysis. Is this true or false?
True
43
Which cells are used to extract nucleic acid from blood and bone marrow aspirates?
WBCs.
44
DNA from WBC can be extracted with:
Hypotonic solutions, were RBC willbe lysed and remain in suspension, while WBC will precipitate, after centrifugation.
45
Exosomes are
Small vesicles originated inside of the cellular endosome containing lipids, proteins and nucleic acid.
46
Proteinase K extended digestion reduces the yield of DNA
False. It increases.
47
List the organic DNA extraction steps
1) lysate cells in suspension with NaOH or SDS;
2) Add acetic acid or Salt to promote sample acidification
3) DNA will be on aqueous solution on top and on bottom will be organic phase
4) Precipitate DNA with ETOH or ISOPROP
5) Ressuspend DNA in buffer or water
48
80% to 90% of the RNA present in the cells are
Ribosomal RNA composed of large and small subunits
49
Total RNA sample is composed of
Ribosomal RNA (80 TO 90%), messenger RNA (2.5 to 5%), transfer RNA and small nuclear RNA
50
What reagent is added to RNA extraction to obtain mRNA?
Single-stranded oligomers of thymine or uracyl
51
What reagent is added to sequence GC rich regions?
dGTP
52
Which subunits of rRNA are visualized on agarose gel?
28S on top (bigger) and 18S on bottom (lighter)
53
Which forms of plasmid DNA is identified on agarose gel?
Supercoiled on bottom, linear above anf nicked or relaxed on top (very faint)
54
Ethidium Bromide and Sybergreen I are utilized to visualize
DNA
55
RNA is best visualized by
Et Br and sybergreen II
56
The Beer-Lambert absorptivity for double-stranded DNA and RNA are
50 for double-stranded DNA and 40 for RNA. The units is ug/mL
57
To find the concentration of a nucleic acid, the formula is
Absorbance x conversion factor = x dilution factor
58
These wavelenghts indicate contamination with
```
230 = organic compounds
260 = phenol
280 = protein
330 = particulate matter
```
59
Less than 1.6 ratio of 260/280 measurement in DNA indicates
Contamination with high levels of proteins
60
DNA preparations with a ratio high than 2.0 indicates contamination with RNA
True
61
Capillary electrophoresis can be used for forensics analysis, patternity testing, clonality testing, microsatelite instability and bone marrow engrafment testing
True
62
What is the purpose of adding formamide + heat to the electrophoresis buffer?
To break hydrogen bonds between DNA RNA strands, preventing from re-anneling
63
Which dyes can be used to detect RNA
Sybergreen II
64
Picogreen, oligreen, hoechst 33258 and sybergreen I are
DNA dyes
65
When a restriction enzyme recognizes one specific sequence but cut on another sequence, this is called
Star activity
66
Restriction Fragment Length Polymorfism (RFLP) is method that utilizes restriction enzymes to map DNA. It is empoyed on
Epidemiological studies (identify microorganisms), forensics (map human DNA) or to identify structural chromosomal changes (translocations, deletions, insertions)
67
Northern blot is used for the following applications
RNA Gene expression analysis and structural abnormalities, such as alternative splicing
68
What is the difference between SDS-PAGE and IEF Western Blotting?
SDS-PAGE resolves protein according to their molecular weight
IEF (IsoElectric Focusing) resolves protein accordingly to their charge
69
The probes used on Southern and Northern blotting are
A single strand nucleotide attached to a signal producing agent
70
Melting temperatures of the probes are calculated using this formula
Tm = 4°C*(# G/C nucleotides) + 2°C*(# A/T nucleotides)
71
dGTP, or Deaza dGTP is used for
Amplification of GC rich regions. It destabilize the secondary structure formed by the GC base pairing
72
What is Taq major advantage:
The ability of continuous cycling through heat steps without losing its enzyme activity
73
Which enzyme is used in reversed transcriptase PCR?
Tth polymerase
74
Which enzyme is recommended to amplify allele specific amplicons and CG rich regions?
Stoffel Fragment, which half life is higher at high temperatures and, has a broader range of MgCl2 concentration requirements
75
What are the steps used in order to avoid PCR contamination?
1. Separate pre and post PCR in different rooms
2. Use of PPE
3. Use positive airflow, airlicks or isolation cabinets
4. Use of UV as decontaminating
5. Use of 10% bleach (7 mM sodium hypochloride)
76
dUTP-UNG sytem will
Degrade any nucleic acid containing uracil when added to the PCR reaction
77
Alkaline phosphatase in combination with exonuclease I enzyme is used for
Removal of nucleotides and primers from PCR products
78
Sequence-specific PCR
Takes advantage of the strict requirements for complementarity of a 3'. Primers are designed to end with a 3' end complementarity for the mutant sequence.
Used in human leukocyte antigen allele analysis for tissue typing
79
Taqman probes have a reporter dye on the 5' and a quencher on the 3'
True
80
A stem and loop structure is formed by the probe in which qPCR system?
Molecular Beacons
81
In FRET, the donor/aceptor probe system will only fluoresce when next to one another on the target sequence
True
82
What metrics should be included when publishing qRT PCR?
Accordingly to MIQE: Target specificity, PCR efficiency, limit of detection, precision, dynamic range, primer sequence and amplicons
MIQE - Minimum Information for Publication of Quantitative Real Time PCR Experiments
83
The use of random degenerative primers throughout the genome or introduction of single strand DNA breaks primed with short hexamers is a hallmark of
Whole Genome Amplification, or WGA
84
In emulsion PCR or Solid Phase Emulsion PCR, the reaction happen in small droplets. Emulsion PCR is used in
Droplet PCR, Sequencing method
85
SDA, or Strand Displacement Amplification, was originally developed to identify
M. tuberculosis, C. trachomatis and N. gonorrhoea
86
Hybdric DNA:RNA assays are used for
Detection of Hepatitis B, HPV and CMV
87
A sequence of nucleotides responsible for a phenotype is called
Genotype
88
Phenotype is defined as
A trait or group of traits resulting of transcription and translation of set of genes
89
A variant that is present in 1 or 2% of the population is considered a polymorfism.
True
90
Examples of benign Polymorfism includes
ABO blood groups, Polymorfisms and major histocompatibility complex used for patternity test and human identification
91
A cell population with a normal chromosomal # is called
Euploid
92
Aneuploids describes
The abnormal number of chromosomes in a cell
93
The region where the chromosomes attach to the spindle apparatus for proper segregation during cell division is called
Centromeres
94
Depending on centromere position, chromosomes can be
Metacentric - middle
Submetacentric - one arm longer than other
Acrocentric - one arm is very small
Telocentric - missing one arm
95
p and q are designations for
Long and short arms of chromosomes, respectively
96
Chromosomes 13, 15, 21 and 22 are considered
Acrocentric or subtelocentric
97
Q banding
Gives intense staining of chromosomes. Especially used to identify chromosome Y
98
The pattern of chromosomal staining obtained with Giemsa is
G pattern
99
Alkaline treatment of chromosomes resulting in centromere staining is also known as
C banding
100
Reciprocal translocations are
Translocations between 2 chromosomes where the broken chromosomes reassociates with one another. Also known as balanced translocations
101
When centromeres are involved in inversions, they are called
Pericentric inversions
102
Philadelphia chromosomes in Leukemia, are a results of
Reciprocal translocations between chromosomes 9 and 22.
103
The term 46, XX del(7)(q13) means
A female with 46 chromosomes and a deletion in the long arm of chromosome 7, region 1 band 3
104
Klinefelter syndrome 47, XXY is
A result of an extra chromosome X in males
105
A chromosome with a centromere located as such that one arm of the chromosome is longer that the other is called
Submetacentric
106
What chromosomal location is indicated by 15q21.1
Long arm of chromosome 15 region 2, band 1 and subband 1
107
How many cells are analyzed on FISH?
500
108
Silent mutations do not change the amino acid sequence
True
109
In conservative mutations,
The amino acid is mutated by another one with the same biochemical property, e.g. polar by polar
110
A mutation that terminates the protein sequence abruptly is designated as
Nonsense mutations. About 11% of the disease causing mutations are nonsense mutations.
111
Mutations in the 3' region have drastic consequences to protein synthesis.
False. Mutation in the 5' have more drastic consequences to protein synthesis.
112
EIA and ELISA stand for
Enzyme ImmunoAssay (EIA) and Enzyme-linked ImmunoAssay (ELISA)
113
Gas chromatography coupled with Mass spectrometry is being used for
Detection of cancer biomarkers, drug detection
114
These two methods areused for the detection of large biomolecules and protens
ESI - Electrospray Ionization
MALDI - Matrix-Assisted Laser Desorption/Ionization
115
When analyzing nucleic acid at a single base pair resolution by MALDI-TOF, these reagebts are used
A primer that binds 5' of the base to be analyzed and ddNTP'S.
116
Sequence detection methods can be classified as
Hybridization methods, sequence methodos and enzyme or chemical cleavage methods.
117
Single Strand Conformation Polymorfism (SSCP) is based on the principle that
DNA and RNA will form intrastrand duplexes to maintain their double strand conformation. Differences in the shape of the conformers are caused by sequence differences, impacting the migration on polyacrylamide gel
118
Sequence-Specific Primer PCR (SSP-PCR) is commonly used for
Detection of point mutations and other SNPs.
119
Heteroduplex is double strand DNA molecule with one or more non complementary base.
True
120
MALDI separates ions by
Mass and charge
121
Cite 3 processing steps undergone by mRNA
Polyadenylation, capping and splicing
122
Heating a digested DNA by including a final incubation at 95 will
Inactivate the restriction enzyme to stop its activity
123
Exons are the parts of the heterogeneous noncoding RNA (hnRNA) that are translated into protein
True
124
Intervening sequences that interrupt protein ciding sequences on hnRNA are
Introns
125
What is a satisfactory ratio A260/A280 for RNA
>2
126
Which reagent is added to sequencing reaction to promotes equal incorporation of all dNTPs by the Polymerase enzyme?
Manganese
127
What are the differences between dye primer and dye terminator sequencing approaches?
Dye primer, the fluorescent dyes are attached to 5', resulting in 4 versions of the primer (one which sequencing color)
On dye terminator, fluorescent dyes are attached to each ddNTP used.
128
Chain termination sequencing or Bisulfite DNA sequencing detect
Methylated cytosine nucleotides
129
What is the acceptable Phred score for sequencing
2 to 3 (100 to 1000 fold certainity of a correct call)
130
The size of the entire genome is
2.91 billion of bp or Gbp
131
Only 2% of the genome code for genes
True
132
Salmonella can only be indentified in urine and stoll after 2 weeks post infection
True
133
The best swab system to collect bacteria, viruses and mycoplasma from mucosal surfaces are
Dacron or calcium arginate swabs with plastic shafts
134
Mycobacteria, fungi, gram-positive bacteria have a thick cell wall
True
135
When using sputum as nucleic acid source, which inhibitor needs to be removed?
Acidic polysaccharides
136
Internal controls for amplification of microorganisms can be
Homologous extrinsic or intrinsic, heterologous extrinsic or intrinsic.
137
Homologous extrinsic are modified versions of the target that maintain the primer binding site
True
138
Homologous intrinsic may be
Smaller, bigger or the same size as the target
139
When validating a new molecular test for microorganism detection, what parameters do we need to include
Sensitivity, specificity and reproducibility
140
LAMP means
Loop-mediated isothermal Amplification
141
16S RNA, 23S RNA, groEL, rpoB, recA and gyrB are genes usefull in the moleculat organism identification
True
142
These are key enzymes involved in DNA replication: Helicase, Single stranded binding proteins, topoisomerase, DNA pol I (RNAse H), DNA pol III, primase (creates RNA primers), DNA ligase
True
