Genetics and Genomics Quiz

Microbial Genetics and Genomics, and Their Applications in Society

• Microbial genetics and genomics are the study of genes and genomes in microbes, and their applications in society
• The flow of information in cells involves DNA replication, transcription, and translation
• DNA replication involves using both strands as templates for the synthesis of new DNA
• In transcription, the dark green strand serves as the template for RNA synthesis
• Translation converts messenger RNA to protein
• In prokaryotes, transcription and translation can occur simultaneously, starting on an mRNA before it is complete

DNA Structure

• DNA has specific base pairing between cytosine and guanine, and adenine and thymine
• The DNA molecule has two anti-parallel strands
• DNA has directional information, usually written as 5' to 3'
• The three-dimensional structure of DNA reveals the major and minor grooves, allowing DNA-binding proteins to find correct sequences for binding
• DNA is compacted in the cell through supercoiling and protein interactions
• E. coli chromosome is 700 times the length of the cell

Genes

• Genes are pieces of nucleic acid that specify a function
• Genes produce mRNAs (translated to make proteins)
• Genes produce tRNAs (involved in protein synthesis)
• Genes produce rRNAs (key components of ribosomes)
• Genes produce other active RNAs (e.g., regulatory, enzymatic)
• Not all genes encode proteins
• Gene structures vary between prokaryotes and eukaryotes
• Prokaryotes can have multiple protein-coding regions on a single mRNA (polycistronic) and typically do not contain introns
• Eukaryotes have one protein-coding region per mRNA and contain introns
• Primary RNA transcripts undergo processing to generate mature mRNA, which includes 5’ caps and poly-A tails
• Splicing removes introns
• Prokaryotic rRNAs also get processed

Transcription - RNA Polymerase

• RNA polymerase is a multi-protein complex
• The promoter region is where RNA polymerase binds, opens the double-stranded DNA and begins transcription
• Termination happens at specific sites in the DNA

Bacterial Sigma Factors

• Bacteria use sigma proteins for promoter recognition
• Sigma is only involved in initiation and released after transcription begins
• Different sigma factors control transcription of different sets of genes in bacteria (e.g., E. coli has 7 sigmas)

Initiation in Archaea and Eukarya

• Archaea and Eukarya use TBP and TFB proteins for promoter recognition
• These proteins bind to the promoter, and then RNA polymerase binds
• Promoters have different sequence properties than bacterial promoters

RNA Polymerases and Evolution

• Archaeal and eukaryotic RNA polymerases are more similar to each other than to bacterial RNA polymerases
• This is consistent with the evolution of the nucleus from an archaeal cell

Transcription Termination

• In bacteria, transcription often stops at inverted repeat sequences
• After transcription, the resulting RNA folds into a stem-loop structure, causing RNA polymerase to detach from DNA

Regulation of Gene Expression

• Some genes are expressed continuously (constitutive genes)
• Most genes are expressed only when needed (regulated genes)
• Different mechanisms regulate gene expression, targeting transcription, translation, or protein activity/stability

Regulation of Transcription Initiation

• First level of control is through sigma and TBP proteins
• Additional DNA-binding proteins control whether RNA polymerase binds to promoters and initiates transcription
• Negative regulators (repressors) inhibit RNA polymerase binding
• Repressors bind to a DNA sequence called an operator
• Positive regulators (activators) stimulate RNA polymerase binding
• Activators bind to a DNA sequence called an activator binding site (ABS)

DNA-Binding Regulatory Proteins

• DNA-binding regulatory proteins interact with DNA at specific sequences
• In prokaryotes, many DNA-binding proteins have a helix-turn-helix structure

Induction

• Induction is common for controlling the expression of catabolic enzymes
• The substrate turns on the gene expression.
• Induction can be controlled by a repressor (negative induction) or an activator (positive induction)
• Lactose catabolism is an example of induction

Negative Induction - lac Operon

• The lac operon (3 genes) controls lactose catabolism
• When no lactose is present, the repressor binds to the operator, blocking transcription
• The repressor protein blocks RNA polymerase

Negative Induction

• When lactose is present, an inducer (allolactose) binds to the repressor
• This causes the repressor to change shape and no longer bind to the operator
• The genes are transcribed

Positive Induction - mal Operon

• The mal operon controls maltose catabolism
• The mal operon requires an activator protein
• The activator protein cannot bind to DNA without the inducer (maltose)

Repression

• Repression is common for controlling the expression of anabolic enzymes
• The product of the reaction/pathway turns off the gene expression.

Repression

• When arginine is present, it binds to the repressor
• The repressor then binds to the operator, stopping transcription

Operons versus Regulons

• Genes for utilizing lactose are in one operon, regulated by the Lacl repressor protein
• Genes for utilizing maltose are found in multiple locations (operons) and regulated by the maltose activator protein

Global Control of Gene Expression

• Cells use catabolite repression to prioritize the use of preferred energy sources over other potentially available resources
• Cells only utilize the second sugar once the first preferred sugar is exhausted

Global Control of Gene Expression

• The phenomenon is called catabolite repression
• Glucose is typically the preferred sugar
• Cells will use glucose first, then switch to lactose if glucose is exhausted

Global Control of Gene Expression

• if lactose is present, why aren't the genes expressed?
• requires the absence of the repressor (Lacl) AND the presence of the activator protein (CRP) bound to its specific DNA sequence

CRP and Catabolite Repression

• CRP (cyclic AMP receptor protein) binds to DNA when bound to cAMP
• cAMP is synthesized by adenylate cyclase
• Glucose inhibits adenylate cyclase, resulting in low cAMP levels and preventing CRP binding to DNA

Regulation by Two-Component Systems

• Two-component systems (TCSs) are a major way bacteria sense and respond to their environment
• TCSs consist of two main proteins: a sensor kinase and a response regulator
• The sensor kinase senses the environmental signal and autophosphorylates

Regulation by Two-Component Systems

– Sensor kinase: Senses environmental signals and phosphorylates itself on a histidine residue, often located in the cytoplasmic membrane – Response regulator: Gets phosphorylated by the sensor kinase and then regulates a cellular process, often by affecting gene expression

Regulation by Two-Component Systems - E. coli Porins

– Sensor kinase EnvZ senses osmotic force – Activated EnvZ-P activates the response regulator OmpR – OmpR controls the transcription of porin protein genes

Chemotaxis

• Chemotaxis is controlled by a complex two-component system
• Cells respond to attractants and repellants by moving toward attractants and away from repellants

Regulation by Quorum Sensing

• Some organisms sense the population density of their species and alter gene expression / behaviors when the population density is high
• QS-regulated behaviors include motility, toxin production, light production, and biofilm formation

Quorum Sensing

• Cells synthesize and release a signal molecule called an autoinducer, which concentration will tell them how many cells are present
• A receptor protein senses the autoinducer and the cell will respond in a specific way
• Different species have different autoinducers

RNA-Based Regulation

• Gene expression is controlled directly via RNA folding and RNA-RNA binding:
• Antisense RNAs alter the RBS (ribosome binding site), and riboswitch, alters the rate of translation
• Attenuation alters the completion of mRNA synthesis

Regulation by Antisense RNAs

• Antisense RNAs can block the ribosome binding site, and translation, and either prevent the degradation of a target mRNA or cause its degradation, preventing translation
• Antisense RNAs can positively or negatively regulate translation

Regulation by Attenuation

• Attenuation alters the completion of mRNA synthesis, often by controlling the formation of a termination loop
• The translation of a leader peptide in the mRNA affects the formation of a termination loop, stopping or continuing transcription.

Operon structure of Trp synthesis

• Attenuation relies on the tryptophan genes and a leader peptide. If there is enough tryptophan the leader peptide will be formed quickly and it will terminate transcription. If tryptophan is low, translation will be slower and transcription will proceed

Plasmids in Prokaryotes

• Plasmids are extrachromosomal, self-replicating DNA molecules
• They exist separately from the chromosome
• They can be circular or linear
• They often carry genes for antibiotic resistance or other specialized functions

Core and Pan Genomes

• Core genomes contain the genes present in all members of a species
• Pan genomes contain all genes found in any member of a species.

Horizontal Gene Transfer in Prokaryotes

• Transformation uptake of free DNA from outside the cell
• Transduction transfer of DNA between cells by viruses
• Conjugation transfer of plasmid DNA between cells

Functional vs. Size in Prokaryote Genomes

• The proportions of genes involved in various cellular functions change with genome size
• Important cellular processes (DNA replication and translation) use large molecular machines, so are a proportionally high percentage in smaller genomes
• The regulation of process is relatively flexible in larger genomes.

Eukaryotic Genomes

• Variation in genome sizes exists amongst eukaryotes, just as with prokaryotes
• Several factors such as the presence and numbers of introns contribute to variation, but there isn't a simple linear relationship with genome size

Applications of Prokaryote Genetics and Biotechnology

• Recombinant DNA technologies use bacteria to make proteins for human use.
• Bacteria produce proteins used in human medicine, such as clotting factors, growth factors.
• Prokaryote genetics is used to make herbicide-resistant plants, insect-resistant plants, and faster growing fish for aquaculture.
• Microbes are manipulated including using them to treat diseases.
• Synthetic or modified genomes/cells

Applications of Metagenomics

• Metagenomics analyzes DNA directly from environmental samples.
• Bio-prospecting new life forms.
• Screening for useful proteins/properties for applications to different areas.

Single-Cell Genomics

• Characterizing individual cells in natural environments without the need for pure cultures.
• DNA sequencing and other analyses directly on individual cells from natural environments

Genome Evolution

• Genomes undergo various types of changes over time, including mutations, gene duplications, deletions, mobile elements, and horizontal gene transfer.

Test your knowledge on key concepts related to lac genes, transposable elements, and genome sequencing. This quiz covers questions about gene expression, cAMP synthesis, chemotaxis, and significant advancements in genomics. Ideal for students studying molecular genetics or genomics.