Molecular Genetics Quiz

Microbial Genetics and Genomics

• Microbial genetics and genomics encompass the study of the genetic material and its applications within various social contexts.
• Chapters 6, 9, 10, 12, 13, and 19 cover related topics.

Information Flow in Cells

• Replication: Both DNA strands serve as templates for new DNA synthesis.
• Transcription: The dark green strand acts as the template for RNA synthesis.
• Translation: Messenger RNA (mRNA) serves as a template for protein synthesis.
• Prokaryotes often exhibit coupled transcription and translation, with translation initiating on an mRNA before it's completely transcribed.

DNA Structure

• DNA's structure features specific base pairing between cytosine and guanine, and adenine and thymine.
• The sugar-phosphate backbone exhibits a helical arrangement of 10 base pairs per turn.
• The major and minor grooves of DNA's three-dimensional structure offer access points for DNA-binding proteins.
• DNA compaction in cells, as seen in E. coli, involves supercoiling and protein interactions, allowing 700 times more DNA length to be fit into the cells.

Genes

• Genes are segments of nucleic acid carrying instructions for specific functions.
• Genes can produce various types of RNA, including mRNA, which is then translated into proteins; tRNA, involved in protein synthesis; rRNA, serving as ribosome components; and other active, regulatory, and enzymatic RNAs.
• Not all genes encode proteins.
• Prokaryotic gene structures differ from eukaryotic gene structures. Prokaryotes can possess multiple protein-coding regions on a single mRNA and usually lack introns.
• A "polycistronic mRNA" contains several genes sequenced on a single transcript. Prokaryotes utilize operons – clusters of co-transcribed genes regulated from a single regulatory region preceding the first gene.
• Eukaryotic genes have single protein-coding regions on one mRNA and typically include introns. Primary RNA transcripts undergo processing—including the addition of 5' caps and poly-A tails—and splicing to remove introns to create mature mRNA.
• Some prokaryotic RNAs also undergo processing, like rRNA components.

Transcription - RNA Polymerase

• RNA polymerase is a multi-protein complex.
• Promoter regions serve as RNA polymerase binding sites, initiating DNA opening and the subsequent transcription process.
• Termination sites establish specific spots for the conclusion of transcription within the DNA sequence.

Bacterial Sigma Factors

• Bacteria employ sigma proteins for promoter recognition during transcription initiation.
• Sigma is involved only in initiation, releasing from the promoter after the transcription process starts.
• Different sigma factors allow the control of gene transcription of diverse genes.

Initiation in Archaea and Eukarya

• Archaea and eukaryotes use TBP and TFB proteins for promoter recognition.
• These bind to the promoter regions before RNA polymerase binding to start transcription.
• Promoters in archaea and eukaryotes exhibit different sequence properties compared to promoters in bacteria.

RNA Polymerases and Evolution

• Archaea and eukaryotic RNA polymerases are structurally more similar to one another compared to bacterial RNA polymerases.
• This structural similarity aligns with the evolutionary lineage of the eukaryotic nucleus arising from an archaeal cell.

Transcription Termination

• In bacterial transcription, termination is commonly triggered by inverted repeat sequences.
• Following transcription of these repeats, the RNA sequence folds into a stem-loop structure, which in turn causes RNA polymerase to detach from the DNA.

Regulation of Gene Expression

• Some genes are constitutively expressed, whereas others are regulated to be expressed only when needed.
• Regulation points encompass transcription, translation, and protein activity/stability.

Regulation of Transcription Initiation

• Transcription initiation control occurs primarily through sigma and TBP proteins.
• Negative regulators (repressors) prevent transcription by inhibiting RNA polymerase binding to DNA.
• Positive regulators (activators) stimulate transcription by enhancing RNA polymerase binding to DNA.

DNA-Binding Regulatory Proteins

• DNA-binding regulatory proteins interact with DNA at specific sequences, often binding to exposed bases in the DNA grooves.
• Many prokaryotic DNA-binding proteins have a helix-turn-helix structure, with one helix binding to the DNA.

Induction

• Induction is a common regulatory mechanism for controlling the expression of catabolic enzymes.
• The presence of an inducer (e.g., a substrate) turns on the expression of a gene or set of genes.
• This process can be controlled via repressors (negative induction) or through activators (positive induction).

Negative Induction - lac Operon

• The lac operon governs lactose catabolism in bacteria.
• Negative induction means absence of the inducer results in repressor binding to the operator, blocking RNA polymerase activity, and thereby preventing gene transcription.

Negative Induction

• When lactose is present, the inducer (allolactose) binds to the repressor, causing a change in shape that prevents the repressor from binding to the operator. This allows transcription to proceed.

Positive Induction - mal Operon

• The mal operon controls maltose catabolism.
• Positive induction requires an activator protein that cannot bind to DNA without an inducer (e.g., maltose) to be present.

Repression

• Repression, common for controlling anabolic enzymes, involves the product of the reaction or pathway turning off the gene's expression.
• With arginine biosynthesis enzymes as an example, when arginine is present, it binds to the repressor, changing its shape so that it can then bind to the operator, thereby stopping transcription.

Operons versus Regulons

• Operons and regulons are gene sets regulated by the same regulator(s).
• Operons containing genes for lactose utilization are regulated by the Lac repressor protein; those for maltose use the maltose activator protein.

Global Control of Gene Expression

• Catabolite repression is a regulatory mechanism where glucose is often utilized before lactose when both are available.

Global Control of Gene Expression (continued)

• In the presence of multiple sugars, cells will utilize one first and then the other once that first sugar source is depleted.

CRP and Catabolite Repression

• CRP, or cyclic AMP receptor protein, binds to DNA only when bound to cyclic AMP.
• Glucose inhibits adenylate cyclase, which synthesizes cAMP, leading to low cAMP levels when glucose is high and vice-versa.
• CRP binding to cAMP enhances RNA polymerase recruitment to promote transcription of the genes for lactose utilization.

Regulation by Two-Component Systems

• Two-component systems (TCS), a common bacterial regulatory mechanism, enable them to sense and respond to environmental stimuli.
• They involve a sensor kinase (often in the cytoplasmic membrane) that senses something and responds by phosphorylating itself on a histidine residue.
• The phosphorylated sensor kinase then interacts with a response regulator, which gets phosphorylated. The phosphorylated response regulator then regulates the expression of downstream genes.

Chemotaxis

• Chemotaxis is controlled by a multi-protein TCS, regulating cell responses to environmental signals.
• The regulator (CheY) controls the rotation of the flagellum to bind to chemoattractants or repellants to direct movement.

Regulation by Quorum Sensing

• Quorum sensing is a regulatory system that allows bacteria to detect and respond to their population density.
• It involves cell signaling with an autoinducer, a molecule produced and released by bacteria to sense the overall density of similar cells.
• Quorum sensing controls several processes, like motility, toxin production, light production, or biofilm formation.

RNA-Based Regulation (continued)

• Antisense RNAs, riboswitches, and attenuation are mechanisms controlling gene expression through interaction or modification of the RNA molecule.

Regulation by Antisense RNAs

• Antisense RNAs can regulate gene expression by either promoting or preventing degradation of a target mRNA.

Regulation by Attenuation

• Attenuation regulates the completion of mRNA synthesis, not its initiation.
• Bacterial mRNA leader sequences and their folding patterns determine whether transcription proceeds or terminates.
• The presence of excess tryptophan leads to a well-defined mRNA secondary structure that terminates mRNA synthesis, preventing transcription of subsequent tryptophan synthesis genes.
• The absence of tryptophan allows transcription to continue producing tryptophan synthesis genes.

Prokaryote Genomics

• Genomics refers to tools that are used in the assessment, analysis, and comparison of genomes. Complete genome maps are now available for >225,000 prokaryotes.
• One early example of a complete cellular genome's sequencing came from Haemophilus influenzae in 1995
• Today, advancements in high-throughput sequencing technologies allow for faster and more cost effective analyses of genomes with significantly more data output than was possible previously.

Genetic Elements in Cells (Continued)

• Prokaryotes typically have circular chromosomes as their primary genetic material, but not always.
• Plasmids are extra-chromosomal elements that are capable of autonomous replication, while a transposable element is a sequence that can move itself to another location in the genome.
• A plasmid's size is substantially smaller than its chromosome.
• Viruses use relatively small genome sizes in comparison to their bacterial counterparts.

Prokaryote and Eukaryote Genome Variation

• Significant variability in genome sizes exists across prokaryotic species, even among free-living forms.
• In prokaryotes, genomics analysis often reveals that there is approximately one gene per 1000 bases.
• Similar to prokaryotes, genome size varies across eukaryotic lineages, however, a linear correlation between gene number and genome size is not always present. A key factor is the variation in the number of introns present in the eukaryotic organism.

Applications of Prokaryote Genetics

• Prokaryotic organisms, their genes, and genomes serve as the cornerstone for genetic engineering and biotechnological applications.
• Recombinant DNA technology facilitates the combination of DNA sequences from different sources to create novel genetic entities, a process that relies on understanding bacterial genetics.
• Specialized plasmid vectors, such as pUC19, help introduce foreign DNA into bacterial host cells and facilitate screening for the introduction of these foreign genetic materials.
• These approaches are employed for producing proteins with human medicinal and agricultural applications.

Engineered Microbes

• Microorganisms can be engineered to exhibit specific properties to facilitate treatments for diseases or for producing proteins with human medicinal and agricultural applications.
• Synthetic gene sequences now allow scientists to insert, move and arrange genes, thereby creating entirely new biological processes.
• Metagenomics allows for the identification of useful genes, and even complete genomes from natural environments that lack readily cultivatable microorganisms, opening avenues to discovering new or improved biological processes for specific applications.

Applications of Metagenomics

• Metagenomics provides a means to study microorganisms that cannot be easily isolated in the laboratory.
• Metagenomics analyses typically involve extracting and sequencing DNA from an environmental sample containing many different microorganisms.
• This approach complements techniques that identify, culture and study individual organisms.

Single-Cell Genomics

• Single-cell genomics focuses on characterizing individual cells from natural environments.
• The method enables characterizing cells to avoid limitations associated with culturing of individual microorganisms in laboratory settings.

Genome Evolution

• Genome evolution encompasses changes in genomes over time, driven by various processes, e.g. mutations and or mechanisms that translocate or move genes between organisms. The rearrangement or duplication of genetic segments within organisms' genome is another mechanism that may lead to changes in their characteristics.
• Mobile genetic elements like viruses, plasmids, and transposons significantly impact genome evolution and variation among organisms.

"Core" versus "Pan" Genomes

• Core genomes represent a species' minimum shared genetic content, while pan genomes encompass the collectively shared and unique genes across all organisms in a species.
• Specific examples showcase the core and pan genomes in species like Salmonella enterica or E. coli, comparing differences and commonalities between various strains of the organism from a genetic perspective.

HGT in Prokaryotes

• Horizontal gene transfer (HGT) is a rapid mechanism for bacterial evolution, contrasting with the relatively slower processes of mutation and gene duplication.
• HGT, a form of genetic exchange, occurs frequently and plays a key role in prokaryotic adaptation and diversification by introducing novel genetic material for selection within the genome.

Transformation

• Transformation is the process by which bacteria introduce foreign DNA from the environment into their genome.
• Some bacterial species naturally have competence - the ability to take up DNA, while other species must be made competent via chemical treatments.

Transduction

• Transduction is DNA transfer between bacteria performed by viruses that infect the bacterial cells.
• Two forms of transduction exist: generalized transduction (any gene segment of the host cell can be transferred) and specialized transduction (specific genes adjacent to the integration site in the host genome).

Conjugation

• Conjugation involves the transfer of plasmid DNA between bacteria via direct cell-to-cell contact and a pilus that forms between the donor and recipient cell.
• The plasmid carrying genes for transfer can be incorporated into the host chromosome, facilitating transfer of entire chromosome regions.

Transposable Elements

• Transposable elements ("jumping genes") are DNA segments capable of moving between different genomic locations.
• Transposable elements are classified into three types – insertion sequences, transposons, and transposable viruses.
• Transposable elements play a substantial role in the generation of variation between closely related strains of bacteria.
• There are many examples of transposable elements in bacteria that insert within existing genetic material or between two adjacent genes, thereby potentially disrupting ongoing function of that genetic material.

Test your knowledge on molecular genetics concepts including lac gene expression, two-component systems, and genome sequencing technologies. This quiz covers key topics relevant to prokaryotic and eukaryotic genetics, as well as advancements in sequencing methods.