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Study Guide: Understanding Plasmids: Structure, Function, and Applications

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Understanding Plasmids: Structure, Function, and Applications Study Guide

Plasmid Fundamentals

Plasmids are extrachromosomal DNA molecules commonly found in bacteria and archaea that can replicate independently.

Answer: True

Explanation: Plasmids are defined as extrachromosomal DNA molecules that exist outside the cell's main chromosome and possess the capability for autonomous replication. They are prevalent in bacteria and archaea.

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The primary role of chromosomal DNA is to contain genes essential for a cell's survival under normal conditions.

Answer: True

Explanation: Chromosomal DNA serves as the primary repository for genes indispensable for a cell's fundamental survival and operation under standard environmental conditions.

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Plasmids, like viruses, are generally classified as living organisms.

Answer: False

Explanation: Plasmids are not generally classified as living organisms; rather, they are genetic elements that are dependent on host cells for their replication and functional expression, similar to viruses.

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Unlike viruses, plasmids are enclosed within a protective protein coat called a capsid.

Answer: False

Explanation: Plasmids, in contrast to viruses, are not enclosed by a protective protein coat known as a capsid; they are composed of 'naked' DNA.

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Naturally occurring plasmids can range in size from very small mini-plasmids to very large megaplasmids.

Answer: True

Explanation: Naturally occurring plasmids exhibit considerable size variation, encompassing entities from diminutive mini-plasmids to extensive megaplasmids.

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What is the fundamental definition of a plasmid?

Answer: A small, extrachromosomal DNA molecule that can replicate independently of the cell's chromosome.

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In which types of organisms are plasmids most commonly found?

Answer: Primarily in bacteria and archaea, but also in eukaryotes.

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What kind of genetic information do plasmids typically carry that is not usually found in chromosomal DNA?

Answer: Additional genes providing special advantages like antibiotic resistance or virulence.

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How does the role of plasmids differ from that of chromosomal DNA within a cell?

Answer: Chromosomal DNA contains essential genes for normal survival, while plasmids contain genes for special traits or advantages in specific circumstances.

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Are plasmids generally classified as living organisms?

Answer: No, they are genetic elements that rely on host cells for replication and function.

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What is the typical size range of naturally occurring plasmids?

Answer: From 1 kilobase pair (kbp) to several megabase pairs (Mbp).

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Plasmid Replication and Maintenance

Plasmids are considered replicons, meaning they are units of DNA capable of replicating autonomously.

Answer: True

Explanation: Plasmids are classified as replicons, signifying that they are discrete units of DNA possessing the inherent capacity for autonomous replication within a suitable cellular environment.

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The plasmid copy number is influenced by how its replication initiation is regulated and its molecular size.

Answer: True

Explanation: The number of plasmid copies maintained within a cell, known as the copy number, is determined by factors such as the regulation of its replication initiation and its overall molecular size.

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Partition systems are mechanisms found in low-copy-number plasmids that ensure distribution to daughter cells.

Answer: True

Explanation: Partition systems are specialized mechanisms present in low-copy-number plasmids, designed to guarantee their equitable distribution into daughter cells during cell division.

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What does the term 'replicon' refer to in the context of plasmids?

Answer: A unit of DNA capable of replicating autonomously within a suitable host cell.

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What are the components of a typical bacterial replicon?

Answer: A gene for a plasmid-specific replication initiation protein (Rep), iterons, DnaA boxes, and an adjacent AT-rich region.

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What is the function of the 'origin of replication' (ori) on a plasmid?

Answer: To serve as the specific stretch of DNA essential for its independent replication within a cell.

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Plasmid Transfer and Classification

Conjugation is the primary method by which plasmids are transmitted between bacteria.

Answer: True

Explanation: Conjugation is recognized as the principal mechanism through which plasmids are transferred between bacterial cells, representing a key form of horizontal gene transfer.

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Conjugative plasmids contain transfer genes to promote conjugation, while non-conjugative plasmids cannot initiate it alone.

Answer: True

Explanation: Conjugative plasmids are characterized by the presence of transfer genes that facilitate conjugation, whereas non-conjugative plasmids lack these genes and are therefore unable to initiate conjugation independently.

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Mobilizable plasmids can transfer at high frequency independently of other plasmids.

Answer: False

Explanation: Mobilizable plasmids require the assistance of conjugative plasmids to transfer at high frequency; they cannot perform this process independently.

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Plasmids are assigned to incompatibility groups based on whether they can coexist in the same bacterial cell.

Answer: True

Explanation: Incompatibility groups are designations for plasmids based on their inability to coexist within the same bacterial cell, typically due to shared replication or partitioning machinery.

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Plasmids are primarily transmitted between bacteria through a process called transformation.

Answer: False

Explanation: The primary mechanism for plasmid transmission between bacteria is conjugation, not transformation, which is typically employed in laboratory settings for DNA introduction.

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Mobilizable plasmids can transfer at high frequency independently of other plasmids.

Answer: False

Explanation: Mobilizable plasmids require the assistance of conjugative plasmids to transfer at high frequency; they cannot perform this process independently.

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Plasmids are assigned to incompatibility groups based on whether they can coexist in the same bacterial cell.

Answer: True

Explanation: Incompatibility groups are designations for plasmids based on their inability to coexist within the same bacterial cell, typically due to shared replication or partitioning machinery.

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Plasmids are primarily transmitted between bacteria through a process called transformation.

Answer: False

Explanation: The primary mechanism for plasmid transmission between bacteria is conjugation, not transformation, which is typically employed in laboratory settings for DNA introduction.

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How are plasmids primarily transmitted from one bacterium to another?

Answer: Via horizontal gene transfer through conjugation.

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What are the two main categories of plasmids based on their ability to transfer between cells?

Answer: Conjugative and Non-conjugative plasmids.

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Functional Categories of Plasmids

Degradative plasmids provide bacteria with the enzymes to digest unusual substances like toluene.

Answer: True

Explanation: Degradative plasmids confer upon bacteria the enzymatic machinery necessary for the catabolism of uncommon substrates, such as toluene.

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Virulence plasmids turn a bacterium into a pathogen by providing genes that help it colonize a host and overcome defenses.

Answer: True

Explanation: Virulence plasmids contribute to pathogenicity by encoding genes that enhance a bacterium's ability to colonize a host and evade host defense mechanisms.

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Cryptic plasmids are known to always provide a clear survival advantage to their host bacteria.

Answer: False

Explanation: Cryptic plasmids do not consistently confer a clear survival advantage to their host bacteria, although recent research suggests potential roles in phenomena like heteroresistance.

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Chromids are genetic elements that exist at the boundary between a chromosome and a plasmid.

Answer: True

Explanation: Chromids are defined as genetic elements situated at the interface between chromosomal and plasmid DNA in certain bacteria.

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Degradative plasmids provide bacteria with the enzymes to digest unusual substances like toluene.

Answer: True

Explanation: Degradative plasmids equip bacteria with the necessary enzymes to metabolize unusual compounds, such as toluene.

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Virulence plasmids turn a bacterium into a pathogen by providing genes that help it colonize a host and overcome defenses.

Answer: True

Explanation: Virulence plasmids contribute to pathogenicity by encoding genes that enhance a bacterium's ability to colonize a host and evade host defense mechanisms.

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Cryptic plasmids are known to always provide a clear survival advantage to their host bacteria.

Answer: False

Explanation: Cryptic plasmids do not consistently confer a clear survival advantage to their host bacteria, although recent research suggests potential roles in phenomena like heteroresistance.

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Chromids are genetic elements that exist at the boundary between a chromosome and a plasmid.

Answer: True

Explanation: Chromids are defined as genetic elements situated at the interface between chromosomal and plasmid DNA in certain bacteria.

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Which of the following is NOT one of the five main functional classifications of plasmids?

Answer: Replicative plasmids

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What do Fertility (F) plasmids contain that enables them to undergo conjugation and express sex pili?

Answer: Specific transfer genes (*tra* genes)

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What is the significance of Resistance (R) plasmids?

Answer: They contain genes conferring resistance to antibiotics, contributing to multidrug resistance.

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What do Col plasmids encode?

Answer: Proteins capable of killing other bacteria (bacteriocins).

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What is the purpose of Degradative plasmids?

Answer: To enable bacteria to digest unusual substances.

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How do Virulence plasmids contribute to a bacterium's pathogenicity?

Answer: By providing genes that help the bacterium colonize a host and overcome its defenses.

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Plasmids in Biotechnology and Research

Artificial plasmids are widely used as vectors in molecular cloning to drive the replication of recombinant DNA sequences.

Answer: True

Explanation: Artificial plasmids are instrumental in molecular cloning, functioning as vectors to facilitate the replication of recombinant DNA sequences within host cells.

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Plasmids are introduced into host cells in a laboratory setting through a process known as transformation.

Answer: True

Explanation: In laboratory environments, the introduction of plasmids into host cells is commonly achieved via a technique termed transformation.

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pMLST is a method used to cluster or type plasmids based on their sequence content.

Answer: True

Explanation: pMLST (plasmid multi-locus sequence typing) is a technique utilized for classifying and typing plasmids by analyzing their sequence content.

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A multiple cloning site (polylinker) on a cloning vector plasmid contains various restriction sites for inserting DNA fragments.

Answer: True

Explanation: A multiple cloning site, or polylinker, on a plasmid cloning vector is characterized by the presence of multiple restriction sites, which are crucial for inserting DNA fragments.

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The antibiotic resistance gene on a cloning vector plasmid acts as a selectable marker.

Answer: True

Explanation: The antibiotic resistance gene present on a cloning vector plasmid serves as a selectable marker, enabling the identification of transformed cells.

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A suicide vector is designed to replicate efficiently in the host cell to ensure stable inheritance.

Answer: False

Explanation: A suicide vector is designed not to replicate efficiently in the host cell; its purpose is to integrate into the host chromosome or be lost, rather than to ensure stable inheritance through replication.

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Insulin is a prominent example of a protein produced using plasmids in bacteria.

Answer: True

Explanation: The production of insulin via recombinant DNA technology in bacteria, utilizing plasmids, is a prominent example of protein synthesis.

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The 2 micron plasmid is found in the common baker's yeast *Saccharomyces cerevisiae*.

Answer: True

Explanation: The 2 micron plasmid is a notable plasmid found in the widely used baker's yeast, *Saccharomyces cerevisiae*.

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pMLST is a method used to cluster or type plasmids based on their sequence content.

Answer: True

Explanation: pMLST (plasmid multi-locus sequence typing) is a technique utilized for classifying and typing plasmids by analyzing their sequence content.

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A multiple cloning site (polylinker) on a cloning vector plasmid contains various restriction sites for inserting DNA fragments.

Answer: True

Explanation: A multiple cloning site, or polylinker, on a plasmid cloning vector is characterized by the presence of multiple restriction sites, which are crucial for inserting DNA fragments.

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The antibiotic resistance gene on a cloning vector plasmid acts as a selectable marker.

Answer: True

Explanation: The antibiotic resistance gene present on a cloning vector plasmid serves as a selectable marker, enabling the identification of transformed cells.

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A suicide vector is designed to replicate efficiently in the host cell to ensure stable inheritance.

Answer: False

Explanation: A suicide vector is designed not to replicate efficiently in the host cell; its purpose is to integrate into the host chromosome or be lost, rather than to ensure stable inheritance through replication.

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Insulin is a prominent example of a protein produced using plasmids in bacteria.

Answer: True

Explanation: The production of insulin via recombinant DNA technology in bacteria, utilizing plasmids, is a prominent example of protein synthesis.

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The 2 micron plasmid is found in the common baker's yeast *Saccharomyces cerevisiae*.

Answer: True

Explanation: The 2 micron plasmid is a notable plasmid found in the widely used baker's yeast, *Saccharomyces cerevisiae*.

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What is the primary use of artificial plasmids in molecular biology?

Answer: To act as vectors for replicating recombinant DNA sequences.

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What is the process called by which plasmids are introduced into host cells in a laboratory setting?

Answer: Transformation

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What is pMLST used for in plasmid research?

Answer: To cluster or type plasmids based on their sequence content, particularly replication machinery genes.

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What is the purpose of the antibiotic resistance gene on a plasmid used as a cloning vector?

Answer: To provide a selectable marker, allowing survival of transformed cells on antibiotic-containing media.

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What is a 'suicide vector' in the context of plasmids?

Answer: A plasmid that cannot replicate in the host cell and must integrate or be lost.

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How are plasmids utilized for protein production?

Answer: By inserting the gene of interest into the plasmid, introducing it into bacteria, and then inducing the bacteria to produce the protein.

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What is a prominent example of a protein produced using plasmids in bacteria?

Answer: Insulin

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Which of the following is a key feature typically found in a plasmid used as a cloning vector?

Answer: A gene conferring antibiotic resistance.

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Historical Context and Terminology

The term 'plasmid' was coined by Joshua Lederberg in 1952.

Answer: True

Explanation: The term 'plasmid' was first introduced and defined by Joshua Lederberg in the year 1952.

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The definition of a plasmid has always exclusively referred to genetic elements outside the chromosome that replicate autonomously.

Answer: False

Explanation: The definition of a plasmid has evolved; initially, it encompassed a broader range of genetic elements, but it was later refined to exclusively refer to extrachromosomal genetic elements that replicate autonomously.

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Who coined the term 'plasmid,' and what was its original definition?

Answer: Joshua Lederberg in 1952, defining it as 'any extrachromosomal hereditary determinant.'

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What was Joshua Lederberg's original definition of a plasmid in 1952?

Answer: Any extrachromosomal hereditary determinant.

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