Viruses, Bacteria, and Archaea Flashcards

Characteristics and Structure of Viruses

• Definition of a Virus: A virus is defined as an infectious particle comprised of a small chromosome that is encapsulated by a protein coat known as a capsid.

• Chromosomal Composition: The genetic material (chromosome) within a virus can be composed of either $ext{DNA}$ or $ext{RNA}$.
      * These chromosomes may be structured as either double-stranded or single-stranded molecules.

• The Viral Envelope: In certain types of viruses, the protein capsid is further surrounded by an outer membrane called an envelope.

• Metabolic and Reproductive Limitations:
      * Viruses possess no internal metabolism.
      * Viruses do not contain organelles.
      * Viruses lack any inherent method of reproducing on their own.

• Mechanism of Reproduction: Viruses reproduce exclusively by entering a host cell and hijacking that cell's machinery to manufacture copies of the virus.
      * Attachment Phase: The process begins when the virus attaches to specific membrane proteins located on the surface of the host cell.
      * Lock and Key Specificity: The attachment mechanism functions via a "lock and key" specificity. This specific interaction limits the host range of the virus, which refers to the specific types of cells, tissues, or species the virus is capable of infecting.
      * Cellular Entry: Methods of entry into the host cell vary by virus:
          * In some instances, only the viral chromosome enters the host cell.
          * In other instances, the entire virus is taken into the host cell through the process of endocytosis.
      * Reproductive Pathways: Once inside the host cell, the virus follows one of two primary pathways: the lytic cycle or the lysogenic cycle.

The Lytic Cycle of Viral Reproduction

• Process Definition: The lytic cycle is a viral reproductive pathway where the host cell actively produces new viruses.

• Outcome: This process typically occurs to such an extreme extent that the host cell eventually bursts (lyses), releasing the new viral particles.

• DNA Viruses in the Lytic Cycle: If a virus possesses a $ext{DNA}$ chromosome, enzymes from the host cell are utilized to express viral genes and replicate the viral chromosome.
      * Example Viral Genes: Genes that code for capsid proteins are typically expressed during this phase.

• RNA Viruses in the Lytic Cycle: Viruses with $ext{RNA}$ chromosomes cannot rely solely on host enzymes; the virus must provide its own enzymes to facilitate gene expression and chromosomal replication.
      * Standard RNA Virus Strategy: Some viruses provide an enzyme that generates a complementary $ext{RNA}$ strand from the original $ext{RNA}$ chromosome.
          * The resulting complementary $ext{RNA}$ functions as $ext{mRNA}$ for viral genes.
          * This same complementary $ext{RNA}$ acts as a template to replicate the original viral chromosome.
      * Retrovirus Strategy: Retroviruses are a specific class of $ext{RNA}$ viruses that provide an enzyme known as reverse transcriptase.
          * Reverse transcriptase creates a complementary $ext{DNA}$ ($ext{cDNA}$) molecule from the viral $ext{RNA}$ chromosome.
          * This $ext{cDNA}$ migrates into the nucleus of the host cell and inserts itself directly into the host's chromosome.
          * Host enzymes then produce complementary $ext{RNAs}$ ($ext{cRNAs}$), which serve as both $ext{mRNAs}$ for the synthesis of viral proteins and as genomic copies for new viral chromosomes.

The Lysogenic Cycle and Latency

• Process Definition: The lysogenic cycle is a reproductive pathway characterized by a period of latency or inactivity.

• Integration: The viral chromosome inserts itself into the host cell's chromosome.

• Latency Phase: Following integration, the virus enters a state of little or no activity, meaning there is minimal gene expression and few, if any, viruses exit the host cell.

• Replication: The integrated viral genes are replicated alongside the host cell's own chromosomes every time the host cell undergoes division.

• Susceptible Viruses: This pathway is exclusive to retroviruses and certain types of $ext{DNA}$ viruses.

• Terminology:
      * The integrated viral $ext{DNA}$ within the host genome is referred to as a provirus or a prophage.

• Cell Survival: During this cycle, the host cell remains alive and continues to function normally, potentially harboring the inactive virus for years.

• Induction of the Lytic Cycle: Specific environmental conditions or stressors can cause a latent virus to become active and enter the lytic cycle.
      * Triggers: Examples of these conditions include exposure to radiation, contact with certain chemicals, or general stress applied to the host organism.

Fundamental Characteristics of Prokaryotes

• Definition: Prokaryotes, which include bacteria and archaea, are organisms characterized by the absence of a nucleus surrounding their genetic material ($ext{DNA}$).

• Unicellular Nature: All prokaryotes are unicellular organisms.

• Chromosomal Structure: They possess a single, circular chromosome.

• Evolutionary and Ecological Status:
      * Prokaryotes were the first life forms to appear on Earth.
      * They represent the most numerous life forms currently on the planet.
      * They exhibit the highest level of diversity in terms of both metabolism and habitat.

• Reproduction: Prokaryotes reproduce rapidly through a process called binary fission.
      * Binary fission involves cell division occurring immediately following the replication of the $ext{DNA}$.
      * Prokaryotes do not engage in sexual reproduction.

Characteristics and Classification of Archaea

• Molecular Composition: Archaea are prokaryotes with cell walls and cell membranes composed of different molecules than those found in bacteria.

• Habitats: Most archaea are extremophiles, meaning they inhabit extreme environments.

• Types of Archaea:
      * Thermophiles: Archaea specifically adapted to live in environments with high temperatures.
      * Acidophiles: Archaea that survive in environments with highly acidic $ext{pH}$ levels.
      * Halophiles: Archaea that thrive in environments with high salt concentrations.
      * Methanogens: Archaea that live exclusively in anaerobic environments (habitats lacking oxygen).
          * Metabolic Output: Methanogens decompose plant and animal wastes to produce methane, which is a flammable gas.

Characteristics and Classification of Bacteria

• Cellular Structure: Bacteria are prokaryotes with cell membranes and cell walls that differ molecularly from those of archaea.

• Distribution: Bacteria are ubiquitous and can be found in nearly every environment on Earth.

• The Bacterial Cell Wall: The wall is composed of peptidoglycan, which consists of sugar chains cross-linked by short polypeptides.

• Gram Staining and Classification: The thickness of the peptidoglycan layer is used as a primary classification method via the Gram stain:
      * Gram-positive bacteria: Possess a thick cell wall that stains purple.
      * Gram-negative bacteria: Possess a thin cell wall that stains pink.

• Morphology: While all bacteria are unicellular, some species are filamentous, meaning the cells link together to form long strands.

• Ecological Roles and Benefits:
      * Cyanobacteria: These bacteria perform photosynthesis.
      * Decomposers: They break down dead organic matter to recycle essential nutrients within ecosystems.
      * Nitrogen-fixing ($N_2$) Bacteria: These organisms convert atmospheric nitrogen gas into a usable form that plants require to synthesize proteins and $ext{DNA}$.

• Pathogenic Bacteria: Certain bacteria are disease-causing agents, such as:
      * Cholera: Found in water contaminated with animal waste.
      * Salmonella: Often found on raw meats.
      * Pneumonia: A bacterial infection that targets the lungs.

Bacterial Genetics and Gene Transfer

• Genomic Organization: A typical bacterium has a single circular chromosome containing a few thousand genes.

• Plasmids: Bacteria may also contain small, circular pieces of $ext{DNA}$ called plasmids, which typically hold fewer than $100$ genes.

• Asexual Reproduction: Reproduction occurs via binary fission, where the chromosome duplicates and the cell divides, resulting in daughter cells with identical genes to the parent cell.

• Horizontal Gene Transfer: Despite being asexual, genes can pass between bacteria through three distinct methods:
      * Transformation: This occurs when a bacterium takes in "naked" foreign $ext{DNA}$ from its environment and incorporates it into its own chromosome. Many bacteria possess specialized membrane transport proteins for this purpose.
      * Transduction: This involves the transfer of genes between bacterial cells via a virus known as a bacteriophage.
          * Occasionally, a bacteriophage may accidentally package the host cell's bacterial $ext{DNA}$ into its capsid instead of viral genetic material.
          * When this abnormal bacteriophage infects a new cell, it delivers the genes from the previous host bacterium to the new one.
      * Conjugation: This is the direct transfer of $ext{DNA}$ between two bacteria using a temporary structure called a sex pilus.
          * The sex pilus acts as a bridge between the cytoplasms of the two linked cells.

Detailed Mechanics of Bacterial Conjugation

• The F Factor: This is a specific group of genes that enables a bacterium to produce a sex pilus and perform the transfer of $ext{DNA}$ to another cell.

• Bacterial Designations:
      * $ext{F}^+$ or $ext{hfr}$: Bacteria that possess the $ext{F}$ factor.
      * $ext{F}^-$: Bacteria that lack the $ext{F}$ factor.

• Location of the F Factor: The $ext{F}$ factor may be located on the bacterial chromosome or on a plasmid.

• Transfer Process: An $ext{F}^+$ bacterium uses its sex pilus to connect to an $ext{F}^-$ bacterium.
      * During the transfer, the $ext{DNA}$ sent to the $ext{F}^-$ cell always includes the $ext{F}$ factor.
      * Upon completion, the recipient $ext{F}^-$ bacterium becomes an $ext{F}^+$ bacterium.
      * Chromosomal Transfer: If the $ext{F}$ factor is integrated into the chromosome, additional genes located near the $ext{F}$ factor may also be transferred to the recipient cell along with the factor itself.

Bacterial Gene Regulation: The Operon

• Definition of an Operon: An operon is a region of the bacterial chromosome comprising several genes (usually part of the same metabolic pathway), a promoter, and an operator.

• Transcription Mechanism: When $ext{RNA Polymerase}$ binds to the promoter, it transcribes a single $ext{mRNA}$ molecule that contains all the genes within the operon.

• Regulation by Repression: The transcription process can be halted by a repressor protein.
      * The repressor protein binds to a specific sequence within the promoter known as the operator.
      * When the repressor is bound to the operator, it physically blocks $ext{RNA Polymerase}$ from attaching to the promoter, thereby stopping transcription.

Mechanisms of Repressor Proteins

• Activity Status:
      * Transcription OFF: Occurs when the repressor is bound to the operator.
      * Transcription ON: Occurs when the repressor is not bound to the operator.

• Allosteric Regulation: The ability of a repressor to bind to the operator is modified by small molecules acting as allosteric regulators.

• Co-repressors:
      * Certain repressors are inactive until they are allosterically activated by a co-repressor.
      * A co-repressor is typically the final product of the metabolic pathway controlled by the operon.
      * Example: The amino acid Tryptophan acts as a co-repressor for the $ext{Trp}$ operon (the operon responsible for synthesizing tryptophan).

• Inducers:
      * Certain repressors are naturally bound to the operator until they are allosterically inhibited by an inducer.
      * An inducer is typically the starting substrate of the metabolic pathway controlled by the operon.
      * Example: The disaccharide Lactose acts as an inducer for the $ext{Lac}$ operon (the operon that enables the bacterium to utilize lactose as an energy source).

Mechanisms of Activator Proteins

• Definition: An activator protein is a protein that increases the rate of transcription by assisting $ext{RNA Polymerase}$ in attaching to the promoter.

• Activity Status:
      * Transcription ON: Occurs when the activator is bound to the promoter.
      * Transcription OFF: Occurs when the activator is not bound to the promoter.

• Example: The CAP Protein: The $ext{CAP}$ protein acts as an activator for the $ext{Lac}$ operon.

• Allosteric Activation: The ability of an activator to bind to the promoter is regulated by small molecules.
      * Example: $ext{cAMP}$: The $ext{CAP}$ protein is allosterically activated by $ext{cAMP}$.
      * Cellular Context: $ext{cAMP}$ is a molecule that is only present in the cell when it is starving for glucose, signaling the need to activate alternative pathways like the $ext{Lac}$ operon.