Molecular Biology Quiz: Transposable Elements

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Questions and Answers

What is the primary function of the enzyme TRANSPOSASE?

To repair damaged DNA

To synthesize RNA

To replicate DNA

To facilitate DNA movement (correct)

Which type of transposable element is the simplest?

Chromosomal integrases

Transposons

Insertion sequences (correct)

Transposable viruses

What additional feature distinguishes transposons from insertion sequences?

Transposable viruses

Ability to integrate into host genomes

Additional genes between IS elements (correct)

Presence of inverted repeats only

What role do transposable elements play in prokaryotic genomes?

They are responsible for variation between strains Signup and view all the answers

Transposons like Tn5 carry genes for which important characteristic?

Antibiotic resistance Signup and view all the answers

What effect do transposable elements (TEs) have when they are inserted into a gene?

They disrupt the gene, usually preventing functional product production. Signup and view all the answers

Which bacterial enzyme is primarily responsible for cutting DNA at specific sequences during recombinant DNA technology?

Restriction enzyme Signup and view all the answers

What is the role of plasmid vectors like pUC19 in cloning?

They allow selection of cells that have taken up the plasmid. Signup and view all the answers

What is the primary function of restriction enzymes in bacteria?

To cut incoming viral DNA into pieces Signup and view all the answers

How does recombinant DNA benefit biotechnology?

It combines pieces of DNA to create new genetic entities. Signup and view all the answers

What is the primary role of attenuation in gene regulation?

It controls the completion of mRNA synthesis. Signup and view all the answers

What determines whether transcription will continue in the regulation by attenuation?

The folding of the leader region in mRNA. Signup and view all the answers

In the context of tryptophan biosynthesis, when is the leader peptide translated quickly?

When tryptophan is abundant in the cell. Signup and view all the answers

What happens to transcription when the leader region is translated slowly due to low tryptophan levels?

Transcription continues without formation of a terminator structure. Signup and view all the answers

What structural element is formed in mRNA when there is plenty of tryptophan present?

A terminator stem-loop. Signup and view all the answers

How do cells regulate tryptophan biosynthesis related to environmental availability?

They synthesize tryptophan only when it is lacking in the environment. Signup and view all the answers

What is the relationship between transcription and translation in attenuation regulation?

Translation can start before transcription is complete. Signup and view all the answers

What is a significant feature of the leader peptide in the regulation of tryptophan biosynthesis?

It contains 2 tryptophan residues. Signup and view all the answers

What does transduction primarily involve in prokaryotes?

Transfer of DNA between cells by viruses Signup and view all the answers

In specialized transduction, what must happen for viral DNA to incorporate host cell DNA?

The virus must integrate itself into the host genome Signup and view all the answers

What characterizes generalized transduction?

Any gene in the cell can potentially be transferred Signup and view all the answers

What role do conjugative plasmids play in bacterial conjugation?

They carry genes that cause the transfer of plasmid DNA between cells Signup and view all the answers

What is the term used to describe a host cell that contains an integrated virus?

Lysogen Signup and view all the answers

What is a crucial step in the process of conjugation between bacterial cells?

Cell-cell contact via a pilus Signup and view all the answers

What happens to arginine biosynthesis genes when arginine is added to the culture?

Their expression is turned off. Signup and view all the answers

What occurs when no arginine is present in the culture?

The biosynthesis genes are transcribed. Signup and view all the answers

Which of the following best describes the process of transduction?

Incorporation of viral DNA into host DNA Signup and view all the answers

How do the genes required for lactose utilization differ from those for maltose utilization?

Maltose genes are regulated by multiple locations. Signup and view all the answers

What mistake can occur during specialized transduction?

The virus improperly cuts itself out of the genome Signup and view all the answers

What is the term for the regulatory mechanism that prioritizes one sugar over another in E. coli?

Diauxic growth Signup and view all the answers

What occurs when both glucose and lactose are available to E. coli?

Glucose is utilized before lactose. Signup and view all the answers

Which of the following statements is true of catabolite repression?

It prevents the expression of lactose usage genes when glucose is present. Signup and view all the answers

What happens to lactose utilization genes when glucose is available?

They remain inactive until glucose is used up. Signup and view all the answers

Which statement best describes a regulon?

A set of operons controlled by the same regulatory factor. Signup and view all the answers

What characteristic allows cells with a functional lacZ gene to form blue colonies?

They can metabolize certain sugars. Signup and view all the answers

Which type of colony is formed by cells containing recombinant plasmid?

White colonies Signup and view all the answers

What is one application of prokaryote genetics mentioned in the content?

Increased milk production in dairy cows Signup and view all the answers

How are engineered microbes being used in cancer treatment?

They are made weaker to target cancer cells specifically. Signup and view all the answers

What process is involved in making synthetic genomes?

Synthesizing large overlapping fragments of a bacterial genome. Signup and view all the answers

What is metagenomics primarily used for?

Bio-prospecting from uncultured microorganisms. Signup and view all the answers

What allows for the screening of colonies with recombinant DNA?

Differences in colony color. Signup and view all the answers

What is a potential benefit of genetically modifying fish in aquaculture?

Faster growth rates. Signup and view all the answers

Study Notes

Microbial Genetics and Genomics, and Their Applications in Society

Microbial genetics and genomics are studied across chapters 6, 9, 10, 12, 13, and 19.
Information flow within cells involves replication, transcription, and translation.

Information Flow in Cells

Replication: Both DNA strands serve as templates for new DNA synthesis.
Transcription: The dark green strand of DNA acts as the template for RNA synthesis.
Translation: Messenger RNA (mRNA) acts as the template for protein synthesis.
Prokaryotic transcription and translation are coupled, meaning that translation can begin on an mRNA molecule before it is complete.

DNA Structure

DNA has a specific base pairing: cytosine with guanine, and adenine with thymine.
DNA strands are antiparallel and directional (5' to 3').
The 3-dimensional structure of DNA exposes bases in major and minor grooves, influencing how DNA-binding proteins find correct sequences to bind.
DNA is compacted through supercoiling and interactions with proteins, about 700 times shorter than its length in a cell.

Genes

A gene is a segment of nucleic acid that specifies a function.
Genes produce mRNA, tRNA, rRNA, and other active RNAs (regulatory and enzymatic).
Not all genes encode proteins.
Prokaryotic gene structures may contain multiple protein-coding regions on a single mRNA (polycistronic) and lack introns.
Eukaryotic gene structures typically consist of one protein-coding region per mRNA molecule and contain introns.
Primary RNA transcripts undergo processing to create mature mRNA, involving 5' caps and poly-A tails, and splicing to remove introns.
Prokaryotic RNAs, such as rRNAs, can also be processed, removing spacers.

Transcription - RNA Polymerase

RNA polymerase is a multi-protein complex.
The promoter region is where RNA polymerase binds, unwinding dsDNA and starting transcription.
Termination occurs at specific sites within the DNA.

Bacterial Sigma Factors

Sigma proteins recognize promoter regions and initiation sites in bacteria.
Sigma proteins are released after initiation of transcription, but different species use different factors to control transcription in response to different conditions.

Initiation in Archaea and Eukarya

Archaea and Eukarya utilize TBP and TFB proteins for promoter recognition and binding. RNA polymerase then binds.
Eukaryotic and Archaeal promoters have different sequence properties compared to bacteria promoters.

RNA Polymerases and Evolution

Eukaryotic and archaeal RNA polymerases are more similar to each other than to bacterial RNA polymerases.
This finding supports the evolutionary relationship between archaea and eukaryotes.

Transcription Termination

Transcription often stops at inverted repeat sequences in bacteria.
The resulting RNA strand folds into a stem-loop structure, causing RNA polymerase to detach from the DNA, stopping transcription.

Regulation of Gene Expression

Some genes are constitutively expressed (always).
Most genes are regulated and only expressed when needed, to control protein production and activity.
There are various mechanisms for regulating gene expression at the level of transcription, translation, and protein activity/stability.

Regulation of Transcription Initiation

The first level of control is typically through sigma and TBP proteins.
Negative regulators, called repressors ,prevent transcription by binding to operator sequences on DNA.
Positive regulators, called activators, stimulate transcription by binding to activator binding sites located near or on promoters.
Regulators interact with specific DNA sequences (promoter, operator, etc).
Repressors and activators function in controlling the initiation of transcription.

DNA Binding Regulatory Proteins

DNA-binding regulatory proteins interact with specific DNA sequences.
In prokaryotes, many proteins have a Helix-Turn-Helix structure.
These often function as dimers and bind to inverted repeat sequences (palindromes) on DNA.

Induction:

Induction is common for controlling the expression of catabolic enzymes.
A substrate turns on the expression of the gene(s) being induced.
Induction can be through repressors (negative induction) or an activator (positive induction).

Negative Induction: lac operon

The lac operon controls lactose catabolism.
In the absence of lactose, the lac repressor binds to the operator DNA, blocking transcription.
In the presence of lactose, lactose binds to the repressor and changes its shape, causing dissociation from the operator, allowing transcription to proceed.

Positive Induction: mal operon

The mal operon controls maltose catabolism.
In the absence of maltose, the activator protein cannot bind to DNA, preventing the initiation of transcription.
When maltose is present, serving as the inducer, it binds to the activator protein, allowing the activator to bind to DNA, thus initiating transcription.

Repression

Repression is used to control the expression of anabolic enzymes.
The final product of the reaction/pathway inhibits further production of the enzyme(s) to prevent excess production of the end products.
When there's sufficient product of the reaction, the final product inhibits further enzyme activity to prevent excess synthesis.

Operons versus Regulons

Operons are clustered genes controlled by a single regulator or operon.
Regulons are sets of genes (often on different locations) that are controlled by a single regulator.
The genes for lactose and maltose utilization illustrate the differences in regulation between prokaryotes.

Global Control of Gene Expression

Catabolite repression is a phenomenon in bacteria where a preferential use of available glucose over other sugars (e.g. lactose) occurs if both are available.
Glucose utilization genes are prioritized.
Cells use a variety of global regulators to adjust gene expression to environmental conditions in response to cellular needs using quorum sensing and two-component systems.

CRP and Catabolite Repression

The CRP protein, or cAMP receptor protein, is an important activator in prokaryotic bacteria
CRP only binds to DNA with cAMP.
Glucose inhibits the enzyme adenylate cyclase, reducing cAMP levels, so high glucose is associated with low cAMP and lack of CRP binding and thus overall reduced gene expression.

Regulation by Two-Component Systems

Two-component systems are protein signaling pathways used by bacteria (and archaea) in response to environmental signals
The two main components are the sensor kinase and the response regulator.
A sensor kinase senses an environmental change, often on the membrane (like osmotic pressure) The kinase autophosphorylates(transfers a phosphate from ATP to itself). The phosphate is then transferred to the response regulator which can then regulate gene expression, often via binding to DNA, turning genes "on" or "off."
An example given is how E. coli controls porin proteins in response to environmental osmotic force.

Chemotaxis

Chemotaxis is regulated by a multi-protein TCS (two-component system). It involves sensing attractants or repellents and responding by altering the rotation direction of the flagellum. The response regulator CheY controls the flagellar rotation.

Regulation by Quorum Sensing

Quorum sensing is a process whereby cells detect the density of other bacteria around them and thus decide whether or not to activate certain genes based on the "population" density.
An autoinducer signalling molecule, is released. It's concentration triggers a response when a critical threshhold is passed to the receptor protein.
The response protein can turn genes on (or off) as necessary, controlling behaviors such as motility, toxin production, light production, and biofilm formation.

RNA-Based Regulation

Antisense RNAs, riboswitches, and attenuation mechanisms regulate gene expression at the level of the RNA itself.

Regulation by Antisense RNAs

RNA folding mechanisms can affect ribosome-binding sites (RBS) availability for translation directly.
Antisense RNA could block an mRNA and prevent its translation or bind to mRNA, thereby freeing an RBS allowing translation.
Antisense RNA can also regulate mRNA degradation, impacting whether or not the mRNA is expressed.

Regulation by Attenuation

Attenuation affects mRNA synthesis.
Involves the "coupling" of transcription and translation to affect the length of the mRNA transcript in cases where the translation is rapidly stalled, which is influenced by the leader peptide (this can then influence whether transcription/gene expression continues or is turned off).
Examples include the control of tryptophan biosynthesis to limit excess tryptophan synthesis.

Microbial Genomics

Genomics encompasses mapping, sequencing, and analyzing genomes (complete genetic material including chromosomes and plasmids).
High-throughput sequencing technologies have dramatically increased its speed and decreased its cost.

Applications of Prokaryote Genetics

The development of recombinant DNA technologies, involving cutting and joining DNA fragments, has allowed for cloning and manipulating DNA segments/genes efficiently.
Restriction enzymes, initially studied as bacterial defense mechanisms, are used for cutting DNA into specific segments, and ligases to join DNA fragments. This combined gives the basis for recombinant techniques.
Applications include making therapeutic proteins, producing proteins for agriculture (e.g., bovine growth hormone), creating herbicide-resistant plants, creating insect-resistant plants, and creating faster growing fish for aquaculture.
Prokaryotes can engineer microbes targeted to treat diseases or be used to make new products/materials.
Prokaryotes have large ranges of genome sizes found in various bacteria.

Metagenomics

Metagenomics allows researchers to analyse DNA taken directly from environmental samples (containing many possibly unculturable microorganisms/species).
DNA from natural communities can be sequenced, assembled, and analysed to learn more about the diversity and properties of the microbes present.

Single-Cell Genomics

Single-cell genomics allows characterizing individual cells from natural environments without needing pure cultures.
Cells can be sorted into small wells and directly sequenced for their genomes, transcriptomes, or proteomes.

Genome Evolution

Genomes change over time via various mechanisms including, but not limited to mutations, gene duplication/deletion, mobile genetic elements and horizontal gene transfer.
Mobile genetic elements (viruses, plasmids, and transposons) can cause major shifts in genome structure of a bacteria.
Horizontal gene transfer moves genetic material between different species.
Prokaryotes have a relatively fast evolution rate due to these mechanisms, in comparison to a species that reproduces via sexual reproduction.

"Core" vs "Pan" Genomes

Core genomes are the set of shared genes that are common to all members of a given species,
Pan genomes are the complete set of genes found across all members of a species or group.

HGT in Prokaryotes

HGT allows for the rapid transfer of genetic material (genes) among prokaryotes. This occurs via several mechanisms, including transformation, transduction and conjugation.
Transformation involves the uptake of free DNA.
Transduction results from transfer via viruses.
Conjugation leads to transfer between cells, mediated by plasmids.

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Test your knowledge about transposable elements, their functions, and roles in molecular biology. This quiz covers key concepts such as transposases, plasmid vectors, and gene regulation mechanisms, providing a comprehensive review of essential topics in biotechnology and genetics.