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Questions and Answers
Which type of restriction enzyme requires two non-palindromic sequences with opposite orientation near each other on the same DNA molecule for recognition?
Which type of restriction enzyme requires two non-palindromic sequences with opposite orientation near each other on the same DNA molecule for recognition?
- Type IIs
- Type III (correct)
- Type II
- Type I
What is the typical length of fragments generated by restriction enzymes that recognize four nucleotide sequences in the human genome?
What is the typical length of fragments generated by restriction enzymes that recognize four nucleotide sequences in the human genome?
- 65000 bp
- 1000 bp
- 260 bp (correct)
- 4100 bp
Which statement is TRUE about Type I restriction enzymes?
Which statement is TRUE about Type I restriction enzymes?
- They cleave DNA at specific locations within the recognition sequence.
- They always cleave DNA on one side of the recognition sequence.
- They cleave DNA at random locations up to 1000 nucleotides away from the recognition sequence. (correct)
- They are most frequently used in molecular cloning.
What is the significance of the Roman numeral in the name of a restriction enzyme?
What is the significance of the Roman numeral in the name of a restriction enzyme?
What is the basis for the difference in fragment lengths generated by restriction enzymes recognizing different length sequences?
What is the basis for the difference in fragment lengths generated by restriction enzymes recognizing different length sequences?
Which of the following is NOT a characteristic of type II restriction enzymes?
Which of the following is NOT a characteristic of type II restriction enzymes?
Why do various sequences digested by the same restriction enzyme yield fragments of various lengths?
Why do various sequences digested by the same restriction enzyme yield fragments of various lengths?
What is the purpose of treating the vector-acceptor with phosphatase?
What is the purpose of treating the vector-acceptor with phosphatase?
In the context of plasmid maps, what happens when the insert is oriented opposite to the CMV promoter?
In the context of plasmid maps, what happens when the insert is oriented opposite to the CMV promoter?
What restriction enzyme is specifically mentioned as forming real clones through its restriction site?
What restriction enzyme is specifically mentioned as forming real clones through its restriction site?
Which of the following describes a potential product of self-ligation of a closed vector?
Which of the following describes a potential product of self-ligation of a closed vector?
What does the term 'double symmetrically closed plasmid-acceptor' imply in plasmid cloning?
What does the term 'double symmetrically closed plasmid-acceptor' imply in plasmid cloning?
What is the purpose of adding a specific antibiotic to agar plates when growing bacteria?
What is the purpose of adding a specific antibiotic to agar plates when growing bacteria?
How does restriction analysis confirm the proper cloning of a new gene?
How does restriction analysis confirm the proper cloning of a new gene?
What characteristic of DNA fragments affects their migration speed in an agarose gel?
What characteristic of DNA fragments affects their migration speed in an agarose gel?
What is the significance of using unique combinations of restriction enzymes in cloning?
What is the significance of using unique combinations of restriction enzymes in cloning?
What is the primary method used to analyze DNA fragment masses after enzymatic digestion?
What is the primary method used to analyze DNA fragment masses after enzymatic digestion?
What is the role of plasmids in bacterial cloning processes?
What is the role of plasmids in bacterial cloning processes?
Why is it important to isolate plasmids from bacterial clones?
Why is it important to isolate plasmids from bacterial clones?
What outcome is expected from the transformation of bacteria using plasmids?
What outcome is expected from the transformation of bacteria using plasmids?
What can be concluded from a successful restriction analysis of a plasmid?
What can be concluded from a successful restriction analysis of a plasmid?
What does the burgundy color indicate on a plasmid map regarding restriction enzyme cleavage?
What does the burgundy color indicate on a plasmid map regarding restriction enzyme cleavage?
Which of the following statements about plasmid maps is correct?
Which of the following statements about plasmid maps is correct?
When designing digestion for cloning a specific DNA fragment, which of the following is NOT a typical step?
When designing digestion for cloning a specific DNA fragment, which of the following is NOT a typical step?
In molecular cloning, what is the main purpose of using restriction enzymes?
In molecular cloning, what is the main purpose of using restriction enzymes?
What does analyzing electrophoresis results allow researchers to determine?
What does analyzing electrophoresis results allow researchers to determine?
What can be inferred if a restriction enzyme has a 'double or multiple cleave' denoted in black on a plasmid map?
What can be inferred if a restriction enzyme has a 'double or multiple cleave' denoted in black on a plasmid map?
When planning a cloning strategy for a DNA fragment, what is the role of the acceptor plasmid?
When planning a cloning strategy for a DNA fragment, what is the role of the acceptor plasmid?
What is the significance of the location marked with the enzyme name followed by a number on the plasmid map?
What is the significance of the location marked with the enzyme name followed by a number on the plasmid map?
Which step is essential for recognizing the products of a cloning procedure?
Which step is essential for recognizing the products of a cloning procedure?
In a molecular cloning experiment, what is often the first action taken with the donor plasmid?
In a molecular cloning experiment, what is often the first action taken with the donor plasmid?
To achieve the correct orientation for the OVA-GFP gene aligning with the CMV promoter (sub-point a), which restriction enzyme combinations can be considered?
To achieve the correct orientation for the OVA-GFP gene aligning with the CMV promoter (sub-point a), which restriction enzyme combinations can be considered?
To attain the opposite orientation of the OVA-GFP gene relative to the CMV promoter (sub-point b), which restriction enzyme combination is appropriate?
To attain the opposite orientation of the OVA-GFP gene relative to the CMV promoter (sub-point b), which restriction enzyme combination is appropriate?
What cloning strategy is suggested if the restriction sites flanking the insert are unavailable?
What cloning strategy is suggested if the restriction sites flanking the insert are unavailable?
Which restriction enzyme could be used for cloning the OVA-GFP insert using a single enzyme?
Which restriction enzyme could be used for cloning the OVA-GFP insert using a single enzyme?
What type of cloning method is associated with using only one restriction enzyme?
What type of cloning method is associated with using only one restriction enzyme?
When analyzing new plasmids constructed using a single enzyme cloning method, what aspect should be considered?
When analyzing new plasmids constructed using a single enzyme cloning method, what aspect should be considered?
Which restriction enzyme combination(s) would result in the OVA-GFP gene being in the same orientation as the CMV promoter?
Which restriction enzyme combination(s) would result in the OVA-GFP gene being in the same orientation as the CMV promoter?
What is a potential limitation of using only one restriction enzyme for cloning?
What is a potential limitation of using only one restriction enzyme for cloning?
What considerations are important when selecting restriction enzymes for cloning?
What considerations are important when selecting restriction enzymes for cloning?
Which statement accurately reflects the relationship between the OVA-GFP gene and the CMV promoter in sub-point b?
Which statement accurately reflects the relationship between the OVA-GFP gene and the CMV promoter in sub-point b?
Flashcards
Type I Restriction Enzymes
Type I Restriction Enzymes
Compound enzymes that cleave DNA randomly far from recognition sites, often containing restriction-modification enzymes.
Type II Restriction Enzymes
Type II Restriction Enzymes
Enzymes that cleave DNA at specific locations near recognition palindromic sequences, commonly used in cloning.
Type III Restriction Enzymes
Type III Restriction Enzymes
Similar to Type I, but require non-palindromic sequences nearby; cleave randomly close to recognition sites.
Restriction Enzyme Nomenclature
Restriction Enzyme Nomenclature
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Palindromic Sequences
Palindromic Sequences
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Average Fragment Length - 4 Nucleotides
Average Fragment Length - 4 Nucleotides
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Average Fragment Length - 6 Nucleotides
Average Fragment Length - 6 Nucleotides
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Agar plates and antibiotics
Agar plates and antibiotics
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Recombinant plasmid identification
Recombinant plasmid identification
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Restriction analysis
Restriction analysis
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Restriction enzymes
Restriction enzymes
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Electrophoretic separation
Electrophoretic separation
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Agarose gel
Agarose gel
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Colony selection
Colony selection
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DNA fragment mass
DNA fragment mass
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PCR method analysis
PCR method analysis
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Plasmid Maps
Plasmid Maps
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HindIII Restriction Site
HindIII Restriction Site
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Cloning Vector
Cloning Vector
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Self-Ligation
Self-Ligation
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Non-functional Vector
Non-functional Vector
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Molecular Cloning
Molecular Cloning
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Insert DNA Fragment
Insert DNA Fragment
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Acceptor Plasmid
Acceptor Plasmid
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Electrophoresis
Electrophoresis
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Cleave Site
Cleave Site
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Base Pairs (bp)
Base Pairs (bp)
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Single Cleave
Single Cleave
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Double Cleave
Double Cleave
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Insert Orientation
Insert Orientation
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CMV Promoter
CMV Promoter
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PstI
PstI
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EcoRI
EcoRI
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BamHI
BamHI
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Restriction Enzyme Combinations
Restriction Enzyme Combinations
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Cloning Strategy
Cloning Strategy
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Single Enzyme Cloning
Single Enzyme Cloning
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Vector Combinations
Vector Combinations
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DNA Fragment Obtaining
DNA Fragment Obtaining
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Study Notes
DNA Vectors (Plasmids)
- Plasmids are non-chromosomal DNA elements
- They control their own replication
- Primarily found in bacteria and some eukaryotes
- Circular, double-stranded DNA
- Size ranges from 1kb to over 100kb
- Plasmid copy number varies depending on the ORI (Origin of Replication) sequence
- Some plasmids can transfer horizontally between bacteria
- Often contain antibiotic resistance genes, providing a survival advantage in hostile environments
Restriction Enzymes
-
Nucleases that hydrolyze phosphodiester bonds between DNA bases
-
Found in bacteria and cyanobacteria
-
Part of a restriction-modification system, protecting cells from foreign DNA
-
Recognize specific palindromic sequences
-
Two main types of enzymes:
- Restriction endonuclease (cleaves DNA)
- Methyltransferase (adds methyl groups to DNA)
-
Modification through methylation protects host DNA from its own restriction enzymes, but foreign DNA is degraded
-
Type II enzymes are commonly used in molecular cloning. They cleave DNA at specific locations near their recognition sequence.
-
Resultant DNA fragments can have:
- Blunt ends (both DNA strands cut at the same point) or
- Sticky ends (DNA strands cut at different points, creating overhangs)
-
Type I enzymes cleave DNA at random locations far from the recognition site.
Molecular Cloning
- Basic technique for constructing and modifying genetic tools
- Used to study gene function and expression
- Traditional molecular cloning involves isolating and amplifying a specific DNA fragment.
- Techniques include restriction digestion, ligation, transformation, and colony screening.
- Basic steps:
- Vector (acceptor) preparation:
- Cutting and opening the vector with restriction enzymes
- Optional: Digesting it with alkaline phosphatase.
- DNA fragment (insert) preparation:
- Cutting out the fragment from another vector
- Ligation (joining) of the vector and insert
- Transformation of bacteria
- Growing bacteria on plates with specific antibiotic
- Selecting bacterial colonies containing the recombinant plasmid
- Identifying the recombinant plasmid (resricted analysis and PCR, for example)
- Vector (acceptor) preparation:
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