Methods to study genes Flashcards
Biochemical methods are applied to the main chemical compounds of genetics —notably DNA, RNA, and protein. True or False
True
A laboratory procedure that determines the order of bases in the genome of an organism in one process.
CHOICES:
Genome sequencing, DNA bar-coding, Data analysis, Whole-genome sequencing, DNA shearing
Genome sequencing
Who discovered genome sequencing?
CHOICES:
Frederick Sanger and his team, Arne Tiselius and his team
Frederick Sanger and his team
Scientists add small pieces of DNA tags, or barcodes, to identify which piece of sheared DNA belongs to which bacteria.
CHOICES:
Genome sequencing, DNA bar-coding, Data analysis, Whole-genome sequencing, DNA shearing
DNA bar-coding
Scientists begin by using molecular scissors to cut the DNA, which is composed of millions of bases: A’s, C’s, T’s, and G’s, into pieces that are small enough for the sequencing machine to read.
CHOICES:
Genome sequencing, DNA bar-coding, Data analysis, Whole-genome sequencing, DNA shearing
DNA shearing
Scientists use computer analysis tools to compare bacterial sequences and identify differences. The number of differences can tell the scientists how closely related the bacteria are, and how likely it is that they are part of the same outbreak.
CHOICES:
Genome sequencing, DNA bar-coding, Data analysis, Whole-genome sequencing, DNA shearing
Data analysis
The bar-coded DNA from multiple bacteria is combined and put in the whole genome sequencer. The sequencer identifies the A’s, C’s, T’s, and G’s, or bases, that make up each bacterial sequence. The sequencer uses the bar code to keep track of which bases belong to which bacteria.
CHOICES:
Genome sequencing, DNA bar-coding, Data analysis, Whole-genome sequencing, DNA shearing
Whole-genome sequencing
One of the advantages of whole-genome sequencing is an individual can create personalized plans to treat disease may be possible based not only on the mutant genes causing a disease, but also other genes in the patient’s genome. True or False
True
Whole-genome sequencing allows genotyping cancer cells and understanding what genes are misregulated allows physicians to select the best chemotherapy and potentially expose the patient to less toxic treatment since the therapy is tailored. True or False
True
The volume of information contained in a genome sequence is vast, hence whole-genome sequencing can be a disadvantage. True or False
True
molecular photocopying that is used to amplify, copy - small segments of DNA.
Polymerase Chain Reaction (PCR)
In a typical PCR experiment, the target DNA is mixed with Taq polymerase, the two oligonucleotide primers, and a supply of deoxyribonucleoside triphosphates (dNTPs) in buffer. True or False
True
used to diagnose diseases, identify bacteria and viruses, match criminals to crime scenes, and biotechnology.
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Polymerase Chain Reaction (PCR)
the process of heating and cooling two single-stranded oligonucleotides with complementary sequences.
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Annealing
a process of separating dsDNA into single strands, which are favorable to DNA hybridization.
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Denature
achieved by using the loosened nucleotides of each base to grow the complementary DNA strand
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Extension
thermal denaturation of dsDNA at 94°C
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Denature
temperature is raised at 72-74°C just below the optimum of Taq polymerase
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Extension
temperature is decreased to 50-60°C which allows primers to attach to complementary sequences
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Annealing
Has 25-35 cycles
CHOICES:
Polymerase Chain Reaction (PCR), Denature, Extension, Annealing
Annealing
Most thermal cyclers can pause at 8°C indefinitely at the end of the cycles. True or False
False - 4°C
The RNA molecule is converted to cDNA molecule and then utilized as template sequence for following PCR reaction
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Reverse-Transcriptase Polymerase Chain Reaction
developed to increase the sensitivity and specificity of PCR
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Nested Polymerase Chain Reaction
accomplished by capturing or isolating each individual nucleic acid molecule present in a sample within many chambers, zones, or regions that can localize and concentrate the amplification product to detectable levels.
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Digital Polymerase Chain Reaction
utilized multiple primer sets in a single PCR reaction to produce amplicons with different sizes.
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Multiplex Polymerase Chain Reaction
nonspecific binding in products due to the amplification of unexpected primer binding
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Nested Polymerase Chain Reaction
capability to examine for different target genes and organisms by one PCR reaction
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Multiplex Polymerase Chain Reaction
developed to amplify RNA target
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Reverse-Transcriptase Polymerase Chain Reaction
evaluating the quantity of DNA and RNA molecules that exists in a sample
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Digital Polymerase Chain Reaction
Monitor the amplification of a targeted DNA molecule during the PCR with the use of fluorescent dyes or fluorophore-containing DNA probes such as Taq man
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Quantitative PCR (qPCR)
the amplification reaction is monitored in “real-time.”
CHOICES:
Nested Polymerase Chain Reaction, Digital Polymerase Chain Reaction, Reverse-Transcriptase Polymerase Chain Reaction, Multiplex Polymerase Chain Reaction, Quantitative PCR (qPCR)
Quantitative PCR (qPCR)
There are mainly two types of DNA analysis in qPCR. One is the dsDNA binding dye chemistry for both specific and nonspecific detection of amplified products, and the other is the fluorophore-linked probes for specific PCR product detection. True or False
True
A method of separating electrically charged substances in a mixture
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Electrophoresis
Father of Electrophoresis
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Arne Tiselius
The matrix in which the biomolecules separation takes place
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Supporting medium
Conduct electricity by running buffer
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Soduim Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Buffer system
Separation is brought about through molecular sieving technique, based on the molecular size of the substances
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Gel Electrophoresis
Gel material acts as a “__________”
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
molecular sieve
Most effective in separating DNA fragments of varying sizes from 100bp to 25kb
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Agarose Gel
The technique is widely used for separating proteins and nucleic acids
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Gel Electrophoresis
used for separating smaller nucleic acids and proteins
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Polyacrylamide Gel
An anionic detergent that breaks disulfide bonds and used for denaturing the proteins
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Soduim Dodecyl Sulfate-PAGE
___________ structure held together by covalent cross-linking of Acrylamide and N,N’-methylene bisacrylamide
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Polyacrylamide Gel
Is a linear carbohydrate polymer composed of repeating units of agarobiose, which consists of alternating units of galactose and 3,6-anhydrogalactose
CHOICES:
Frederick Sanger, Arne Tiselius, Supporting medium, molecular sieve, Gel Electrophoresis, Sodium Dodecyl Sulfate-PAGE, Agarose Gel, Polyacrylamide Gel, Agarose Gel, Buffer system, Electrophoresis
Agarose Gel
Factors that Determine the Rate of Migration of a DNA molecule Through a Gel:
A linear DNA fragment of a given size migrates at different rates through gels containing different concentrations of agarose
CHOICES:
Electrophoresis Buffer, Size of the molecule, DNA conformation, Agarose concentration, Presence of DNA stains in the gel electrophoresis buffer, Types of agarose, Voltage applied
Agarose concentration
Factors that Determine the Rate of Migration of a DNA molecule Through a Gel:
Supercoiled circular DNA, relaxed circular DNA and linear DNA of the same molecular weight will migrate at different rates through the gel
CHOICES:
Electrophoresis Buffer, Size of the molecule, DNA conformation, Agarose concentration, Presence of DNA stains in the gel electrophoresis buffer, Types of agarose, Voltage applied
DNA conformation
Factors that Determine the Rate of Migration of a DNA molecule Through a Gel:
The molecular size of nucleic acid is expressed in molecular weight equivalent to the number of bases/ base pairs in the molecule
CHOICES:
Electrophoresis Buffer, Size of the molecule, DNA conformation, Agarose concentration, Presence of DNA stains in the gel electrophoresis buffer, Types of agarose, Voltage applied
Size of the molecule
Factors that Determine the Rate of Migration of a DNA molecule Through a Gel:
Dyes used to stain DNA in gels are usually intercalating agents and Addition to the gel may retard the rate of migration of the DNA
CHOICES:
Electrophoresis Buffer, Size of the molecule, DNA conformation, Agarose concentration, Presence of DNA stains in the gel electrophoresis buffer, Types of agarose, Voltage applied
Presence of DNA stains in the gel electrophoresis buffer
Factors that Determine the Rate of Migration of a DNA molecule Through a Gel:
Various types of agaroses are used for specialized applications
CHOICES:
Electrophoresis Buffer, Size of the molecule, DNA conformation, Agarose concentration, Presence of DNA stains in the gel electrophoresis buffer, Types of agarose, Voltage applied
Types of agarose
Factors that Determine the Rate of Migration of a DNA molecule Through a Gel:
The rate of migration is proportional to the voltage applied, ↑voltage ↑rate of migration
CHOICES:
Electrophoresis Buffer, Size of the molecule, DNA conformation, Agarose concentration, Presence of DNA stains in the gel electrophoresis buffer, Types of agarose, Voltage applied
Voltage applied
Factors that Determine the Rate of Migration of a DNA molecule Through a Gel:
The composition and ionic strength affects DNA mobility, If water electrical conductivity is minimal, then DNA will migrate slowly, However, if the ionic strength is higher (10X Buffer), then the electrical conductance is efficient
CHOICES:
Electrophoresis Buffer, Size of the molecule, DNA conformation, Agarose concentration, Presence of DNA stains in the gel electrophoresis buffer, Types of agarose, Voltage applied
Electrophoresis Buffer
Gels that have a low melting temperature melts at 55 degrees celsius. True or False
False - 65 degrees celsius
Standard gels melt at 90-95 degrees celsius. True or False
True
Insertion of a fragment of RNA carrying genre into a cloning vector and subsequent propagation of recombinant DNA molecules into many copies is known as gene cloning. True or False
False - Insertion of a fragment of RNA carrying genre into a cloning vector and subsequent propagation of recombinant DNA molecules into many copies is known as gene cloning
Gene cloning involves using viruses to make multiple copies of a gene. True or False
False - bacterias
Southern and Northern blot hybridizations are used to hybridize a labeled probe to fractionated and immobilized DNA (Southern) or RNA (Northern). True or False
True
A complex DNA sample is digested with restriction endonucleases. The resulting fragments are applied to an agarose gel and separated by size using electrophoresis.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Southern blot hybridization
A variant of Southern blotting in which the samples contain undigested RNA instead of DNA.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Northern blot hybridization
Is an immunoblotting technique which rely on the specificity of binding between a molecule of interest and a probe to allow detection of the molecule of interest in a mixture of many other similar molecules.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Western blot
uses samples of total RNA or purified poly(A)+ mRNA from tissues or cells of interest.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Northern blot hybridization
Used to identify target sequences that are similar but not identical to the gene used as a probe.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Southern blot hybridization
The principal use of this method is to obtain information on the expression patterns of specific genes.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Northern blot hybridization
the molecule of interest is a protein and the probe is typically an antibody raised against that particular protein.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Western blot
________ use a nylon or nitrocellulose membrane matrix onto which nucleic acid probes have been deposited. Samples are radioactively labeled and hybridized in parallel. Detection is best accomplished through phosphorimaging
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Macroarrays
___________ use a silicon or plastic matrix and a fluorescence-based labeling scheme in which both control and experimental samples are hybridized to the same array in a competitive manner. Fluorescent scanners are used for detection.
CHOICES:
Southern blot hybridization, Northern blot hybridization, Western blot, Eastern blot, Microarrays, Macroarrays
Microarrays
