DNA Vectors and Restriction Enzymes Quiz  8

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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?

  • 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?

  • 65000 bp
  • 1000 bp
  • 260 bp (correct)
  • 4100 bp

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?

<p>It specifies the order in which the enzyme was isolated from a given strain. (D)</p> Signup and view all the answers

What is the basis for the difference in fragment lengths generated by restriction enzymes recognizing different length sequences?

<p>The frequency of occurrence of the recognition sequence in the genome varies with sequence length. (D)</p> Signup and view all the answers

Which of the following is NOT a characteristic of type II restriction enzymes?

<p>They cleave DNA at random locations far from the recognition sequence. (B)</p> Signup and view all the answers

Why do various sequences digested by the same restriction enzyme yield fragments of various lengths?

<p>The frequency of occurrence of each recognition sequence is not consistent in the genome. (D)</p> Signup and view all the answers

What is the purpose of treating the vector-acceptor with phosphatase?

<p>To eliminate vector self-ligation (B)</p> Signup and view all the answers

In the context of plasmid maps, what happens when the insert is oriented opposite to the CMV promoter?

<p>The vector remains non-functional (D)</p> Signup and view all the answers

What restriction enzyme is specifically mentioned as forming real clones through its restriction site?

<p>HindIII (A)</p> Signup and view all the answers

Which of the following describes a potential product of self-ligation of a closed vector?

<p>Vector without an insert (A)</p> Signup and view all the answers

What does the term 'double symmetrically closed plasmid-acceptor' imply in plasmid cloning?

<p>The plasmid has identical ends for ligation (A)</p> Signup and view all the answers

What is the purpose of adding a specific antibiotic to agar plates when growing bacteria?

<p>To inhibit the growth of plasmid-free bacteria. (B)</p> Signup and view all the answers

How does restriction analysis confirm the proper cloning of a new gene?

<p>By analyzing DNA fragment sizes from restriction enzyme digestion. (A)</p> Signup and view all the answers

What characteristic of DNA fragments affects their migration speed in an agarose gel?

<p>The size of the DNA fragments. (A)</p> Signup and view all the answers

What is the significance of using unique combinations of restriction enzymes in cloning?

<p>To create distinctive DNA fragment patterns for different plasmids. (B)</p> Signup and view all the answers

What is the primary method used to analyze DNA fragment masses after enzymatic digestion?

<p>Gel electrophoresis. (C)</p> Signup and view all the answers

What is the role of plasmids in bacterial cloning processes?

<p>They act as vectors for inserting new genes. (C)</p> Signup and view all the answers

Why is it important to isolate plasmids from bacterial clones?

<p>To identify which plasmids contain the desired recombinant DNA. (C)</p> Signup and view all the answers

What outcome is expected from the transformation of bacteria using plasmids?

<p>The bacteria will develop new traits provided by the plasmids. (C)</p> Signup and view all the answers

What can be concluded from a successful restriction analysis of a plasmid?

<p>The cloning event was successful, confirmed by unique DNA fragment sizes. (B)</p> Signup and view all the answers

What does the burgundy color indicate on a plasmid map regarding restriction enzyme cleavage?

<p>The enzyme cleaves the plasmid at a single site (A)</p> Signup and view all the answers

Which of the following statements about plasmid maps is correct?

<p>The beginning of a plasmid is aligned at the 'twelve o'clock' position (B)</p> Signup and view all the answers

When designing digestion for cloning a specific DNA fragment, which of the following is NOT a typical step?

<p>Performing a PCR amplification of the fragment (A)</p> Signup and view all the answers

In molecular cloning, what is the main purpose of using restriction enzymes?

<p>To isolate specific DNA fragments for cloning (A)</p> Signup and view all the answers

What does analyzing electrophoresis results allow researchers to determine?

<p>The size and integrity of DNA fragments after digestion (B)</p> Signup and view all the answers

What can be inferred if a restriction enzyme has a 'double or multiple cleave' denoted in black on a plasmid map?

<p>It can cleave the plasmid in more than one location (C)</p> Signup and view all the answers

When planning a cloning strategy for a DNA fragment, what is the role of the acceptor plasmid?

<p>To serve as the vector for inserting the target DNA fragment (B)</p> Signup and view all the answers

What is the significance of the location marked with the enzyme name followed by a number on the plasmid map?

<p>It points to the specific nucleotide sequence cleaved by the enzyme (D)</p> Signup and view all the answers

Which step is essential for recognizing the products of a cloning procedure?

<p>Analyzing the results of electrophoresis after digestion (D)</p> Signup and view all the answers

In a molecular cloning experiment, what is often the first action taken with the donor plasmid?

<p>Selecting appropriate restriction enzymes for cleavage (A)</p> Signup and view all the answers

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?

<p>PstI / XmaI (C)</p> Signup and view all the answers

To attain the opposite orientation of the OVA-GFP gene relative to the CMV promoter (sub-point b), which restriction enzyme combination is appropriate?

<p>EcoRI / BamHI (C)</p> Signup and view all the answers

What cloning strategy is suggested if the restriction sites flanking the insert are unavailable?

<p>Introducing the missing sites through PCR amplification. (C)</p> Signup and view all the answers

Which restriction enzyme could be used for cloning the OVA-GFP insert using a single enzyme?

<p>XmaI (D)</p> Signup and view all the answers

What type of cloning method is associated with using only one restriction enzyme?

<p>Blunt-end Cloning (A)</p> Signup and view all the answers

When analyzing new plasmids constructed using a single enzyme cloning method, what aspect should be considered?

<p>The orientation of the insert within the vector. (C)</p> Signup and view all the answers

Which restriction enzyme combination(s) would result in the OVA-GFP gene being in the same orientation as the CMV promoter?

<p>PstI / XmaI only (B)</p> Signup and view all the answers

What is a potential limitation of using only one restriction enzyme for cloning?

<p>It does not allow for directional cloning. (B)</p> Signup and view all the answers

What considerations are important when selecting restriction enzymes for cloning?

<p>All of the above. (D)</p> Signup and view all the answers

Which statement accurately reflects the relationship between the OVA-GFP gene and the CMV promoter in sub-point b?

<p>The gene and promoter are transcribed in opposite directions. (B)</p> Signup and view all the answers

Flashcards

Type I Restriction Enzymes

Compound enzymes that cleave DNA randomly far from recognition sites, often containing restriction-modification enzymes.

Type II Restriction Enzymes

Enzymes that cleave DNA at specific locations near recognition palindromic sequences, commonly used in cloning.

Type III Restriction Enzymes

Similar to Type I, but require non-palindromic sequences nearby; cleave randomly close to recognition sites.

Restriction Enzyme Nomenclature

Enzymes are named using the host's first letter and species' first two letters, followed by strain details and a Roman numeral.

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Palindromic Sequences

Sequences that restriction enzymes, especially Type II, recognize; often four to eight bases long.

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Average Fragment Length - 4 Nucleotides

Enzymes that recognize 4-bp sequences generate fragments averaging 260 base pairs long.

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Average Fragment Length - 6 Nucleotides

Enzymes recognizing 6-bp sequences generate fragments averaging 4100 base pairs long; GC specific can yield 65000 bp.

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Agar plates and antibiotics

Agar plates are used to culture bacteria by adding an antibiotic, allowing only resistant bacteria to grow.

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Recombinant plasmid identification

Isolating plasmids from bacterial colonies to confirm proper cloning and resistance gene insertion.

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Restriction analysis

A method to analyze DNA fragments from plasmid digestion using restriction enzymes for cloning verification.

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Restriction enzymes

Proteins that cleave DNA at specific sequences, determining the size of resulting DNA fragments.

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Electrophoretic separation

A technique for separating DNA fragments in agarose gel based on size after restriction digestion.

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Agarose gel

A gel used in electrophoresis to separate DNA fragments by size during restriction analysis.

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Colony selection

Picking specific bacterial colonies from agar plates to isolate plasmids for analysis.

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DNA fragment mass

The size of DNA pieces produced by restriction enzyme cleavage, key in identifying clones.

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PCR method analysis

Polymerase Chain Reaction is used for amplifying DNA to verify the presence of specific sequences in recombinant plasmids.

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Plasmid Maps

Diagrams that show the layout of a plasmid, including restriction sites and features.

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HindIII Restriction Site

A specific DNA sequence where the enzyme HindIII can cut the DNA, used in cloning.

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Cloning Vector

A DNA molecule used to carry foreign genetic material into a host cell for replication.

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Self-Ligation

The process where a plasmid rejoin its ends without inserting foreign DNA, creating a closed vector without an insert.

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Non-functional Vector

A plasmid that cannot express a gene due to incorrect orientation of the insert or no insert present.

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Molecular Cloning

The process of creating copies of a specific DNA fragment.

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Insert DNA Fragment

A specific DNA piece targeted for cloning into a plasmid.

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Acceptor Plasmid

The plasmid that receives the insert DNA fragment.

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Electrophoresis

A technique for separating DNA fragments by size.

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Cleave Site

The specific location on DNA where an enzyme cuts.

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Base Pairs (bp)

The units used to measure the length of DNA.

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Single Cleave

A cut made by an enzyme at one site on a plasmid.

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Double Cleave

Multiple cuts made by an enzyme on a plasmid.

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Insert Orientation

The direction in which a DNA fragment is inserted into a plasmid.

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CMV Promoter

A viral promoter commonly used to drive expression in various cells.

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PstI

A restriction enzyme used to cleave DNA at specific sites.

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EcoRI

A restriction enzyme that recognizes and cuts DNA at the GAATTC sequence.

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BamHI

A restriction enzyme that cuts DNA at the GGATCC sequence.

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Restriction Enzyme Combinations

Different pairs of restriction enzymes used for DNA cloning.

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Cloning Strategy

The method used to insert DNA fragments into vectors.

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Single Enzyme Cloning

Cloning that uses only one restriction enzyme for an insert.

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Vector Combinations

The possible configurations of plasmids when inserting DNA fragments.

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DNA Fragment Obtaining

The process of isolating a specific segment of DNA for cloning.

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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)

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