Microbial Genetics and DNA Structure Quiz
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Questions and Answers

What are the two main types of nucleic acids?

  • Carbohydrates and Lipids
  • Proteins and Lipids
  • DNA and RNA (correct)
  • DNA and Proteins

    • What types of molecules are translated to make proteins?

  • mRNAs (correct)
  • tRNAs
  • rRNAs
  • All of the above

    • All genes encode proteins.

    False

    What is the name of a cluster of co-transcribed genes in prokaryotes that are controlled by a regulatory region?

    <p>Operon</p> Signup and view all the answers

    Eukaryotes typically have polycistronic mRNAs.

    <p>False</p> Signup and view all the answers

    What is the name of the region where RNA polymerase binds to DNA and initiates transcription?

    <p>Promoter</p> Signup and view all the answers

    What is the function of the sigma protein in bacteria?

    <p>Promoter recognition</p> Signup and view all the answers

    The sigma protein remains bound to RNA polymerase throughout the entire transcription process.

    <p>False</p> Signup and view all the answers

    What are the two proteins that Archaea and Eukarya use for promoter recognition?

    <p>TBP and TFB</p> Signup and view all the answers

    Archaeal and eukaryotic RNA polymerases are more closely related to bacterial RNA polymerases than they are to each other.

    <p>False</p> Signup and view all the answers

    What common feature of prokaryotic gene regulation involves controlling the completion of mRNA synthesis, but not the initiation?

    <p>Attenuation</p> Signup and view all the answers

    What is the name for the regulatory proteins that inhibit binding of RNA polymerase to the promoter?

    <p>Repressors</p> Signup and view all the answers

    What is the name of the DNA sequence where repressors bind?

    <p>Operator</p> Signup and view all the answers

    What is the name of the regulatory proteins that promote binding of RNA polymerase to the promoter?

    <p>Activators</p> Signup and view all the answers

    What is the name of the DNA sequence where activators bind?

    <p>Activator binding site</p> Signup and view all the answers

    Activator binding sites must be located directly next to the promoter region.

    <p>False</p> Signup and view all the answers

    What is the common structure found in many prokaryotic DNA binding proteins that bind to the major groove of DNA?

    <p>Helix-turn-helix</p> Signup and view all the answers

    Which of th following describe events that can turn on or off gene expression?

    <p>Induction</p> Signup and view all the answers

    What type of gene regulation is commonly found in the control of catabolic enzymes?

    <p>Induction</p> Signup and view all the answers

    Repression is a regulatory mechanism that is often used to control the production of anabolic enzymes?

    <p>True</p> Signup and view all the answers

    What is the name of the regulatory protein that regulates the expression of the lac operon?

    <p>LacI repressor</p> Signup and view all the answers

    What is the name of the molecule that binds to the LacI repressor and causes it to change shape, allowing transcription of the lac operon?

    <p>Inducer</p> Signup and view all the answers

    Positive induction involves the binding of an activator protein to the promoter region.

    <p>True</p> Signup and view all the answers

    What is the name of the activator protein that regulates the expression of the mal operon?

    <p>MalT activator protein</p> Signup and view all the answers

    A regulon refers to a group of genes or operons that have the same regulatory protein, ensuring that all genes are controlled by the same factor?

    <p>True</p> Signup and view all the answers

    What is the name of the phenomenon where cells utilize different sugars sequentially, leading to distinct growth phases in a batch culture?

    <p>Diauxic growth</p> Signup and view all the answers

    What is the name of the regulatory mechanism that controls gene expression in response to the presence of glucose?

    <p>Catabolite repression</p> Signup and view all the answers

    In catabolite repression, what intracellular molecule plays a critical role in regulating gene expression?

    <p>cAMP (cyclic AMP)</p> Signup and view all the answers

    What is the name of the protein that binds to cAMP and then to specific promoter regions, aiding in the regulation of gene expression?

    <p>CRP (cyclic AMP receptor protein)</p> Signup and view all the answers

    What are the two main components that make up a two-component system (TCS) in bacteria?

    <p>Sensor kinase and Response regulator</p> Signup and view all the answers

    What is the function of the sensor kinase in a TCS?

    <p>Sensing and phosphorylating itself</p> Signup and view all the answers

    What is the function of the response regulator in a TCS?

    <p>Getting phosphorylated and regulating gene expression</p> Signup and view all the answers

    What is the name of the process by which bacteria communicate and coordinate their behavior based on cell density?

    <p>Quorum sensing</p> Signup and view all the answers

    What is the name of the signaling molecule that bacteria release and that accumulates as cell density increases?

    <p>Autoinducer</p> Signup and view all the answers

    When the autoinducer concentration reaches a threshold, it binds to a receptor protein, triggering a signaling cascade within the cell.

    <p>True</p> Signup and view all the answers

    What is the name of the common type of autoinducer molecule found in bacteria?

    <p>AHL (acyl homoserine lactone)</p> Signup and view all the answers

    Which of the following are examples of behaviors regulated by quorum sensing?

    <p>Motility</p> Signup and view all the answers

    What are the three main mechanisms of RNA-based regulation?

    <p>Antisense RNA, Riboswitches, and Attenuation</p> Signup and view all the answers

    What is the name of the specific sequence on an mRNA that binds to ribosomes and initiates translation?

    <p>RBS (ribosome binding site)</p> Signup and view all the answers

    Antisense RNA can block the RBS, preventing ribosome binding and blocking translation.

    <p>True</p> Signup and view all the answers

    Antisense RNA can also bind to the target mRNA and protect it from degradation, leading to increased translation.

    <p>True</p> Signup and view all the answers

    What is the name of the mechanism where a leader region in an mRNA can fold into different structures, affecting the termination of transcription?

    <p>Attenuation</p> Signup and view all the answers

    What is the name of the complete genetic makeup of an organism, including its chromosome(s) and any plasmids?

    <p>Genome</p> Signup and view all the answers

    What is the name of the field of study that involves mapping, sequencing, analyzing, and comparing genomes?

    <p>Genomics</p> Signup and view all the answers

    What is the name of the technology that has enabled a significant increase in genome sequencing, allowing for the rapid sequencing of large DNA fragments?

    <p>High-throughput sequencing (HTS)</p> Signup and view all the answers

    What is the term for extrachromosomal self-replicating DNA molecules found in prokaryotes?

    <p>Plasmids</p> Signup and view all the answers

    Most prokaryotes have linear chromosomes.

    <p>False</p> Signup and view all the answers

    Endosymbionts and parasitic organisms tend to have smaller genomes compared to free-living species.

    <p>True</p> Signup and view all the answers

    The size of a prokaryotic genome is directly proportional to the number of genes, meaning larger genomes always have more genes.

    <p>True</p> Signup and view all the answers

    What are the main ways that genomes change over time?

    <p>Mutations</p> Signup and view all the answers

    Gene duplication can lead to the evolution of new genes with novel functions.

    <p>True</p> Signup and view all the answers

    Horizontal gene transfer is a process that involves movement of genetic material between different organisms through reproduction.

    <p>False</p> Signup and view all the answers

    What are the three main mechanisms of horizontal gene transfer in prokaryotes?

    <p>Transformation, Transduction, and Conjugation</p> Signup and view all the answers

    What is the name for the process where cells take up free DNA from their environment?

    <p>Transformation</p> Signup and view all the answers

    What is the name for the process of transferring DNA between cells using viruses as vectors?

    <p>Transduction</p> Signup and view all the answers

    What is the name of the process of transferring plasmid DNA between cells through direct contact?

    <p>Conjugation</p> Signup and view all the answers

    Conjugative plasmids carry genes that are essential for the transfer process, including the pilus formation.

    <p>True</p> Signup and view all the answers

    What are the mobile genetic elements that can move from one location to another in a genome, known as "jumping genes"?

    <p>Transposable elements</p> Signup and view all the answers

    What are the three main types of transposable elements?

    <p>Insertion sequences (IS), Transposons (Tn), and Transposable viruses</p> Signup and view all the answers

    What is the name of the enzyme encoded by transposable elements that is responsible for their movement?

    <p>Transposase</p> Signup and view all the answers

    Insertion sequences (IS) are the simplest transposable elements, containing only the transposase gene and inverted repeats.

    <p>True</p> Signup and view all the answers

    Transposons are more complex than insertion sequences and often contain additional genes beyond the transposase gene and inverted repeats.

    <p>True</p> Signup and view all the answers

    What is the term for the process of combining two or more pieces of DNA into a new genetic entity?

    <p>Recombinant DNA technology</p> Signup and view all the answers

    Restriction enzymes, which are produced by bacteria, cut DNA at specific sequences, acting as a defense mechanism against viruses.

    <p>True</p> Signup and view all the answers

    What is the main application of metagenomics in studying microbial communities?

    <p>Bioprospecting</p> Signup and view all the answers

    Single-cell genomics allows scientists to study the genetic material of individual cells from natural environments without the need to culture them in the laboratory.

    <p>True</p> Signup and view all the answers

    The pan genome of a species refers to the total collection of genes found in all strains of that species.

    <p>True</p> Signup and view all the answers

    Study Notes

    Microbial Genetics and Genomics, and Their Applications in Society

    • Microbial genetics and genomics cover the study of genes in microorganisms and their genomic applications in society.
    • Chapters 6, 9, 10, 12, 13, and 19 cover this topic.

    Information Flow in Cells

    • DNA replication involves using both strands as templates to create new DNA.
    • Transcription uses a DNA strand as a template to create RNA. RNA polymerase creates the RNA.
    • Translation uses mRNA as a template for protein synthesis. Ribosomes perform this process.
    • Prokaryotes can couple transcription and translation, initiating translation before transcription is complete.

    DNA Structure

    • DNA has specific base-pairing: Cytosine with Guanine and Adenine with Thymine.
    • DNA strands are antiparallel.
    • The double helix has a 3' to 5' directionality.
    • The 3D structure exposes bases in major and minor grooves, crucial for DNA-binding protein recognition.
    • DNA is compacted in the cell through supercoiling and protein interactions. Bacterial chromosomes are typically 700x longer than the cell itself.

    Genes

    • Genes are segments of nucleic acid specifying functions.
    • Genes produce mRNAs (translated into proteins), tRNAs (involved in protein synthesis), rRNAs (ribosomal components), and other active RNAs (regulatory/enzymatic).
    • Not all genes encode proteins.
    • Prokaryotic genes can have multiple coding regions on one mRNA (polycistronic). They do not usually have introns
    • Eukaryotic genes typically have exons, introns, and undergo processing (5' caps, poly-A tails, and splicing) to create mature mRNA.

    Prokaryote Gene Organization

    • Some prokaryotic RNAs undergo processing to remove spacers in the original primary transcript.
    • Example: rRNAs (ribosomal RNA), which are key components of ribosomes

    Transcription - RNA Polymerase

    • RNA polymerase is a multi-protein complex.
    • Promoters are regions where RNA polymerase binds, opens dsDNA, and initiates transcription.
    • Transcription termination occurs at specific sites on the DNA.

    Bacterial Sigma Factors

    • Bacteria use sigma proteins for promoter recognition.
    • Sigma factors are only involved in initiation and are released after transcription begins.
    • Different sigma factors control the transcription of various sets of genes. Example: E. coli has 7 different sigma factors.

    Initiation in Archaea and Eukarya

    • Archaea and Eukarya use TBP and TFB proteins for promoter recognition.
    • These proteins bind to promoters, then RNA polymerase binds.
    • Promoters in Archaea and Eukarya have different sequence properties than those present in Bacteria.

    RNA Polymerases and Evolution

    • Archaeal and eukaryotic RNA polymerases are more similar to each other than to bacterial RNA polymerases.
    • This observation supports the evolutionary relationship between archaea and eukaryotes.

    Transcription Termination

    • Bacteria often terminate transcription at inverted repeat sequences.
    • The resultant RNA folds into a stem-loop structure, causing RNA polymerase to detach.

    Regulation of Gene Expression

    • Some genes (constitutive genes) are expressed continuously, while others are regulated and expressed only when needed.
    • Regulation points include transcription, translation, and protein activity/stability.
    • Various mechanisms control protein production.

    Regulation of Transcription Initiation

    • Sigma and TBP proteins control the initial phase of transcription.
    • Negative regulators (repressors) inhibit RNA polymerase binding, whereas positive regulators (activators) stimulate it.
    • Repressors bind to operator sequences, while activators bind to activator-binding sites.

    Regulators bind to DNA sequences

    • Repressors bind to a DNA sequence called an operator, located between the promoter and the gene(s).
    • Activators bind to a DNA sequence called an activator-binding site (ABS). The ABS can be next to the promoter or farther away.

    DNA-binding Regulatory Proteins

    • DNA-binding proteins in prokaryotes often have a helix-turn-helix structure, with one helix interacting with the DNA grooves in the dsDNA.
    • DNA-binding proteins may function as dimers and bind to inverted repeat sequences.

    Induction

    • Induction is common for control of the expression of genes encoding catabolic enzymes, where a substrate turns on gene expression.
    • Induction is sometimes controlled by repressor (negative induction) or by an activator (positive induction). Lactose metabolism is one example of induction.

    Negative Induction - lac operon

    • The lac operon (3 genes) controls lactose catabolism by negative induction.
    • No lactose: repressor is bound to the operator, genes are not transcribed.
    • Presence of lactose: inducer binds to repressor, altering shape; no more repressor binding to operator; expression of genes proceed.

    Positive Induction - mal operon

    • The maltose operon is controlled by positive induction.
    • No maltose: activator protein cannot bind to DNA; no transcription.
    • Maltose present: Inducer (maltose) binds to activator protein, enabling it to bind to DNA; activates transcription.

    Repression

    • Repression is common for controlling the expression of genes encoding anabolic enzymes.
    • Presence of a product shuts off gene expression (e.g., arginine biosynthesis).
    • Corepressor (product) binds to repressor, enabling it to bind to the operator; transcription stops.

    Operons versus Regulons

    • Cells may have a set of genes/operons controlled by the same regulator called a regulon.
    • An example is the set of genes controlling lactose and maltose which are regulated by separate but related mechanisms.

    Global Control of Gene Expression

    • Cells employ strategies to handle multiple sugars available.
    • If glucose is present, the cells use glucose preferentially and switch to another sugar when it is consumed (diauxic growth).
    • This phenomenon is known as catabolite repression.

    Global Control of Gene Expression

    • The cells first consume the better food source--glucose--before switching to another sugar such as lactose.
    • Catabolite repression is a global regulation mechanism. There are often levels of expression of a particular gene depending on many conditions.

    Global control of gene expression

    • If lactose is present, why aren't the lactose genes expressed?
    • Lactose needs to be present and glucose needs to be absent/exhausted for the expression of lactose utilization genes.

    CRP and Catabolite Repression

    • CRP (cyclic AMP receptor protein) binds to DNA only when bound to cAMP.
    • Glucose inhibits adenylate cyclase (enzyme that produces cAMP).
    • Low glucose: High cAMP, CRP binds to promoter; transcription continues.
    • High glucose: Low cAMP, CRP cannot bind; transcription is inhibited.

    Regulation by Two-Component Systems

    • Two-component systems (TCS) are common in prokaryotes and archaea; they often exist in eukaryotes.

    • TCSs regulate a cell’s response to various environmental stimuli, such as changes in oxygen levels, osmotic pressure, etc.

    • The sensor kinase senses an environmental signal (e.g., osmotic pressure) and phosphorylates itself. The response regulator is then phosphorylated by the sensor kinase and goes on to regulate another target protein.

    Chemotaxis

    • Chemotaxis, directional movement of bacterial cells towards or away from (chemically defined) stimuli, is a complex two-component system.
    • The signal is sensed and the response done through a multi-protein TCS.

    Regulation by Quorum Sensing

    • Bacteria use quorum sensing to respond to changes in population density (density-dependent regulation).
    • Quorum sensing systems involve quorum-sensing proteins which react to the amount of autoinducer present to regulate certain functions that occur only in a large enough population. Some examples of these types of functions are motility, toxin production, biofilms and light production.

    RNA-based regulation

    • Gene expression is directly controlled via RNA folding and RNA-RNA binding.
    • Some examples include antisense RNAs, riboswitches, and attenuation. Antisense RNAs block ribosome binding sites to prevent translation. Riboswitches are specific RNA sequences that bind to small molecules to regulate gene expression. Attenuation controls the completion of mRNA synthesis, not the beginning.

    Regulation by Antisense RNAs

    • Anti-sense RNAs regulate gene expression by either blocking ribosome binding sites (RBS) to prevent translation, binding to the mRNA and freeing the RBS, or promoting mRNA degradation. Specific type of regulation includes mRNA degradation/protection where anti-sense RNAs block the RBS and prevent translation.

    Regulation by Attenuation

    • Attenuation regulates the completion of mRNA synthesis.
    • Transcription begins at the promoter as long as a particular region cannot fold into a terminator stem-loop.
    • The leader region can fold into different secondary structures. This folding is influenced by the presence and amount of the molecule of interest. The structure formed determines if the transcription will be continued or stopped.
    • Examples of proteins controlled in this manner are tryptophan biosynthesis. 

    Microbial Genomics

    • Genome - complete genetic material of an organism, including chromosomes and plasmids.
    • Genomics the mapping, sequencing, and comparison of genomes.
    • First full genome sequenced from Haemophilus influenzae - 1995, hundreds of thousands more have since been sequenced.

    Specific Applications of Microbial Genomics

    • Metagenomics allows for analyzing genomes of a community of microbes in a sample.
    • Proteomics allows identification of proteins in a sample using mass spectrometry.
    • Transcriptomics looks at the RNA present in a sample.

    Genome Evolution

    • Genomes change over time through mutations, gene duplications, gene deletions, mobile elements, and horizontal gene transfer.
    • Mobile genetic elements, such as viruses, plasmids, and transposons, cause large genomic changes.

    Horizontal Gene Transfer

    • Horizontal gene transfer (HGT) is the movement of genetic material from one organism/cell to another.
    • HGT is a key force in bacterial evolution and can occur through three mechanisms: Transformation, Transduction, and Conjugation.

    "Core" vs "Pan" Genomes

    • Core genome: minimal set of genes shared by all cells of a species.
    • Pan genome: the collection of all genes found in all cells of a species. The variation between these genes may be small, but they can be very relevant as the core genes are necessary but there may be additional genes that give the cell a particular adaptation or allow it to carry out novel biochemical functions.

    Core and Pan Genomes: Examples

    • Examples of core and pan genomes are found in strains of Salmonella enterica. E.coli strains are also a relevant useable application.

    HGT in Prokaryotes

    • HGT methods include Transformation, Transduction, and Conjugation.
    • Transformation involves the uptake of free DNA by a recipient cell.
    • Transduction involves the transfer of DNA from one cell to another by viruses.
    • Conjugation involves the transfer of DNA from a donor cell to a recipient cell through a pilus.

    Transposable Elements

    • Transposable elements (TEs) are DNA segments that move within a genome.
    • Three categories: insertion sequences (IS), transposons (Tn), and transposable viruses.
    • TEs cause genomic changes or mutations in the genome.

    Applications of Prokaryotic Genetics

    • Recombinant DNA technology is used to combine DNA pieces from different sources and create novel genetic materials by creating transgenic organisms.

    • Restriction enzymes are bacterial enzymes that cut DNA at specific sequences, enabling use in recombinant DNA Technology.

    • Specialized vectors like pUC19 are used in the study of cloning and manipulating DNA sequences in E. coli.

    • Engineered microbes are used in treating diseases and other medical applications, in agricultural applications, and in industrial uses.

    Applications of Metagenomics

    • Metagenomics enables analysis of uncultured microbes in environmental samples.
    • By analyzing community rather than a species, you have a broader perspective of the functions that microbes in nature may carry out.

    Single-cell Genomics

    • Single-cell genomics is a valuable method to evaluate the variability of a community of cells.
    • Single-cell genomics techniques allow evaluating individuals from a community, without need of producing a pure culture.

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    Microbial Genetics PDF

    Description

    This quiz covers key concepts in microbial genetics, genomics, and DNA structure as explored in chapters 6, 9, 10, 12, 13, and 19. Test your understanding of DNA replication, transcription, translation, and the unique features of DNA. Perfect for students looking to solidify their knowledge in genetics and molecular biology.

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