Uworld Bio - Prokaryotes and Viruses (esidahi)

Similarities btw proks and Euks

- Both have double-stranded DNA - Both of their mRNAs can be bound by multiple ribosomes in the cytoplasm - Under anaerobic condition, glycolysis, fermentation and gluconeogenesis are active in both Euks and Proks - Because the processes do not require O2, - For both, Krebs cycle and the ETC are only active in the presence of a final electron acceptor, such as oxygen (aerobic respiration) or inorganic ions (anaerobic respiration). - Both Euks and Proks are able to reproduce sexually. Sexual reproduction in eukaryotic cells occurs via fusion of gametes (products of meiosis), and prokaryotic cells reproduce sexually through conjugation.

Educational objective: Retroviruses are enveloped, positive-sense, single-stranded RNA viruses that convert their RNA genomes into double-stranded DNA using the enzyme reverse transcriptase. During their lysogenic cycles, retroviruses enter the nucleus and integrate their reversed transcribed DNA with the host genome.

- Retroviruses can integrate viral dsDNA (not +ssRNA) into the host genome. - Because the genome of HXV is +ssRNA, the synthesis of a complementary strand would produce a −ssRNA molecule with no usable functions; therefore, it neither codes for proteins nor integrates into the host genome. - In addition, if the viral ssRNA strands were to hybridize and form a dsRNA molecule, it also could not integrate into the host genome because viral dsRNA has to be converted into dsDNA for incorporation into the host genome.

Characteristics of viruses

- viruses are obligate intracellular parasites that cannot reproduce outside of a host cell - The genetic material of viruses can be RNA or DNA that is double-stranded or single-stranded - genetic material is surrounded by a protective protein coat known as the capsid. - can also be classified as either enveloped (have a phospholipid bilayer as the cell membrane) or nonenveloped (no phospholipid bilayer). - Enveloped viruses have a membrane, or phospholipid bilayer, generally derived from the cell membrane of the host. The phospholipid bilayer of enveloped viruses surrounds the capsid and often contains host-derived proteins, allowing the virus to better evade the immune system and gain entry into the host cell. - nonenveloped (naked) viruses lack a phospholipid bilayer. In contrast, all prokaryotic and eukaryotic cells are enclosed by a phospholipid bilayer.

Lytic life cycle

1) Attachment: The bacteriophage comes in contact with the bacterial cell wall and attaches to the host bacterium using its tail fibers. 2) Viral genome entry: The phage uses its tail sheath to inject its genome into the cytoplasm of the bacterial host 3) Host genome degradation: Viral enzymes degrade the host genome into its nucleotide components to provide the building blocks for replication of the viral genome 4) Synthesis: Loss of the bacterial chromosome ends synthesis of host molecules. As a result, the host machinery (eg, ribosomes), now under the control of the viral genome, begins to synthesize the components needed for new viral progeny, which then assemble inside the host cell. 5) Release: Many newly assembled viral progeny (virions) are released as the bacterium disintegrates (lysis) due to the action of lysozymes on the host cell wall.

Bacteriophages

All viruses are obligate intracellular parasites because they cannot replicate independently outside of a host cell. Bacteriophages are viruses that exclusively infect bacteria. The life cycle of a particular bacteriophage can be lytic or lysogenic, which will determine the method by which the phage uses the host's cellular machinery to create new progeny. Educational objective: Bacteriophages use the host cell's machinery and resources to replicate their genome and synthesize viral proteins to form new virions. Phages with a lytic life cycle replicate rapidly and release progeny via lysis of the host cell. In contrast, phages with a lysogenic life cycle integrate their genome with the host genome and replicate as the cell divides.

Capsids and sensitivity to heat, detergents, and changes in moisture.

All viruses contain - a protective protein coat, called the capsid, composed of individual capsomere subunits. Advantages of having a phospholipid bilayer surrounding the capsid - the envelope helps the virus evade the immune system and contains envelope proteins required for cellular entry. Disadvantages - However, enveloped viruses are sensitive to heat, detergents, and changes in moisture. In contrast, non-enveloped or naked viruses have only a capsid as a protective outer layer and are more resistant to heat, detergents, and changes in moisture.

Animal cell plasma membranes contain;

Animal cell plasma membranes contain; - phospholipids, - cholesterol, - glycolipids (lipids with attached sugar groups), - glycoproteins (proteins with attached sugar groups), and - other proteins.

Diff btw Bacteria, Archaea, Eukarya

Bacteria - Unicellular - Nucleus Absent - Organelles Absent - Cell wall with peptidoglycan Present - Cellular division by Binary fission - Circular Chromosome Archaea - Unicellular - Nucleus Absent - Organelles Absent\ - Cell wall with peptidoglycan Absent - Cellular division by Binary fission - Circular Chromosome Eukarya - Unicellular or multicellular - Nucleus Present - Organelles Present - Cell wall with peptidoglycan Absent - Cellular division by Mitosis - Linear Chromosome

Bacteriophages, Prions and Viroids

Bacteriophages are viruses that exclusively infect bacteria but do not enter host cells to replicate their genetic material. Instead, they use their tail sheath, a structure that injects the phage genome into a bacterium. The remaining viral structures of the phage, such as the tail fibers, the capsid, and the tail sheath, are left outside the bacterium. A prion is a misfolded protein that acts as an infectious agent by inducing other normal proteins to change their secondary structure and become misfolded. These less soluble misfolded proteins aggregate and can cause disease. Prions do not contain genetic material and cannot transform bacteria Viroids are not viruses; instead, they are pathogenic, circular, single-stranded RNA molecules lacking protein coats and primarily affect plants. They typically silence the expression of specific genes and inhibit protein synthesis by binding RNA sequences. Viroids enter cells by hiding inside viruses or through damaged tissue; they do not use the mechanisms described in the question. Educational objective: Bacteriophages are viruses that exclusively infect bacterial cells. They contain tail fibers that allow them to recognize and attach to the cell membrane, and a tail sheath that injects the viral genome into the bacterium. Viroids and prions are considered subviral particles because they are smaller in size and complexity compared to viruses.

The endosymbiotic theory

Educational objective: The endosymbiotic theory explains how primitive eukaryotic anaerobes engulfed ancient aerobic prokaryotes, and consequently acquired the ability to produce energy through oxidative phosphorylation. eg - The discovery of Cu/Zn SODs in other free-living bacterial species with known eukaryotic symbiotic hosts reinforces the hypothesis of eukaryotic to prokaryotic gene transfer. - discovery of Cu/Zn SODs in other free-living bacterial species with no known eukaryotic symbiotic hosts would argue against the hypothesis of eukaryotic to prokaryotic gene transfer due to symbiosis.

Enveloped viruses - enter cell by fusing their membranes with the cell membrane

Enveloped viruses enter cell by fusing their membranes with the cell membrane. - Viruses with a capsid encased in a phospholipid membrane - When this occurs, no vesicle is formed and the capsid is released directly into the cytosol. Therefore, a drug that inhibits fusion of viral and cell membrane would likely prevent the virus from entering cells.

ribosome in cytoplasm ribosome-protein complex → to the rough ER (RER) → to the Golgi body → plasma membrane→outside the cell.

Eukaryotic protein synthesis begins on free ribosomes in the cytoplasm. The secretory pathway involves the processing of proteins as they go through the endoplasmic reticulum and the Golgi apparatus. The presence of a signal sequence on the nascent polypeptide directs the ribosome-protein complex → to the rough ER (RER). The growing polypeptide chain is threaded into the RER lumen and the signal sequence is removed. The peptide is then packaged into vesicles and sent to the Golgi body, where proteins designed for secretion undergo biochemical modifications and are packaged into transport vesicles destined for the plasma membrane. These vesicles then fuse with the plasma membrane and release their contents outside the cell.

Fermentation & Gluconeogenesis - do not require O2, therefore are active in both Euks and Proks

Fermentation - metabolizes pyruvate under anaerobic conditions to oxidize NADH to NAD+ - Fermentation yields lactic acid in the muscles of Euks and alcohol in bacteria. Gluconeogenesis - is the process by which noncarbohydrate carbon sources are converted into glucose. - Because both processes do not require O2, fermentation and gluconeogenesis are active in both Euks and Proks

Differences btw Proks and Euks

For Proks - genetic information is contained within a circular chromosome of double-stranded DNA that has NO telomeres - DNA is NOT associated with histone proteins. - Have NO Introns - lacks membrane-bound organelles - prokaryotic cells duplicate via binary fission, - Have no nucleus; therefore, due to the lack of this physical barrier between DNA and the ribosomal machinery, transcription and translation occur simultaneously in the cytoplasm (ie, translation begins before the mRNA is fully transcribed). - mRNA is translated by the 70S ribosome. - ETC is located on the plasma membrane. - under anaerobic conditions, ATP synthase is active in Proks - Fermentation yields alcohol in bacteria. For Euks - genetic information is contained within a linear chromosomes of double-stranded DNA capped by telomeres to prevent DNA from unravelling - DNA is associated with histone proteins. - Have Introns - Have membrane-bound organelles - Most eukaryotic cells (except germ cells) undergo cell division via mitosis. - Have nucleus; therefore transcription and post-transcriptional modifications occur in the nucleus, but translation occurs in the cytoplasm. - mRNA is translated by the 80S ribosome - ETC is located in the inner mitochondria membrane. - under anaerobic conditions, ATP synthase is not active in Euks - Fermentation yields lactic acid in the muscles of Euks

Lysogenic life cycle

In contrast, bacteriophages that have a lysogenic life cycle also attach to the bacterium but integrate their genome into the host DNA and are called prophages. This viral genome integration enables the host cell to survive and divide normally. While the host cell divides, the integrated viral DNA is replicated with the host DNA, and associated viral repressor proteins prevent the viral genome from being transcribed (latency). Induction can occur in response to environmental factors (eg, chemicals, radiation), causing the viral genome to excise itself from the host chromosome and enter the lytic life cycle.

ETC in Euks is in Inner Mit Membrane ETC in Proks is on Plasma membrane

In eukaryotes, cellular respiration continues when pyruvate is imported into the mitochondria and converted into acetyl-CoA, which then enters the Krebs cycle (citric acid cycle) to generate the necessary electron carriers (NADH and FADH2) for the electron transport chain (ETC). ETC protein complexes pump protons across the inner mitochondrial membrane, generating a proton gradient, with O2 as the terminal electron acceptor. Prokaryotes have no mitochondria; instead, the ETC is located on the plasma membrane.

Sizes of organisms

In order of size from largest to smallest - eukaryotic cells - 10-100 µm in diameter - prokaryotic cell is - 0.5-2 µm in diameter - bacteriophage/HIV virus - 150nm A light microscope has a resolution of 200 nm (0.2 µm); consequently, investigators can use it only to observe cells larger than 0.2 µm. Educational objective: - Proks are 10X smaller than Euks cells. - Viruses are 100X smaller than Proks and 1,000X smaller than Euks. - Unlike bacteria, viruses cannot be observed with a light microscope because viral particles are smaller than the microscope's maximum resolution.

Non-enveloped viruses - enters cells by receptor-mediated endocytosis

Non-enveloped viruses enters cells by receptor-mediated endocytosis, - in which the virus binds specific receptor proteins on the cell surface. - This binding induces the plasma membrane to bud inward toward the cytosol before pinching off as a vesicle that contains both the ligand and its receptor. Therefore, a drug that inhibits this inward budding would likely prevent the virus from entering cells.

Phospholipids, Transmembrane proteins, Cholesterol

Phospholipids Cell membranes are composed largely of phospholipids, which act as a fluid that allows other membrane components such as transmembrane proteins, glycoproteins, cholesterol, and glycolipids to migrate through this environment laterally. Accordingly, the structure of the animal cell membrane is known as the fluid mosaic model. Transmembrane proteins The phospholipid bilayer of the cell membrane has an outer leaflet that interacts with the extracellular environment and an inner leaflet that interacts with the cytoplasm of the cell. Transmembrane proteins cross the entire phospholipid bilayer and therefore interact with both the outer and inner leaflets. Proteins that interact with only one leaflet are not transmembrane proteins. Cholesterol, - which is found in eukaryotic but not prokaryotic cell membranes, functions to regulate the fluidity of the bilayer. Due to their unique structure, cholesterol molecules decrease fluidity at higher temperatures and increase fluidity at lower temperatures. As eukaryotic cells, intestinal epithelial cell membranes contain cholesterol.

Eukaryotic cells - Cell types - Animals, plants, fungi - Size ~10-30 µm DNA - Multiple linear chromosomes - Double-stranded - Multiple origins of replication - Diploid or greater - Telomeres - Located in nucleus - Membrane-bound organelles - Cellular respiration in cytoplasm (anaerobic) & mitochondria (aerobic) - Cell wall (eg, contains cellulose in plants & chitin in fungi) - Ribosomes - 80S ribosomes (composed of 60S & 40S subunits) - Cell division - By Mitosis (cell replication) & meiosis (gamete production)

Prokaryotic cells - Cell types - Bacteria, Archaea - Size ~1-5 µm - DNA - Single circular chromosome - Double-stranded - Single origin of replication - Haploid - No telomeres - Located in cytoplasm - No membrane-bound organelles - Cellular respiration in cytoplasm (aerobic & anaerobic) - Cell wall (eg, contains peptidoglycan in bacteria) - Ribosomes - 70S ribosomes (composed of 50S & 30S subunits) - Cell division - By Binary fission

Classification of bacteria

Prokaryotic organisms such as bacteria can be classified by their shape, or morphology. The morphology-based classification of bacteria involves three basic shapes: Bacilli are rod-shaped bacteria. Cocci are spherical bacteria. Spirilli are spiral bacteria. This method of classification enables physicians to identify bacteria easily based on their appearance under a light microscope. Habitat refers to the natural environment in which an organism resides. Classification according to habitat typically uses the suffix -philes. Bacteria tend to inhabit numerous environments; for example, some bacteria can be thermophiles (comparatively high temperatures), acidophiles (low pH), or halophiles (high Oxygen dependence is determined by a bacterium's ability to use fermentation, anaerobic respiration, aerobic respiration, or some combination of these to generate ATP from various nutrients.

Retrovirus

Retrovirus - are integrated with the host genome (DNA). - Retroviruses are unique in that they are enveloped and carry two identical +ssRNA molecules. Successful viral replication depends on enzymes that allow its viral genome (RNA) to enter the nucleus and integrate with the host genome (DNA). Retroviruses enter host cells through endocytosis, which allows the capsid and envelope to uncoat (disassemble). - Uncoating releases the viral genetic material inside the host cell. RNA viruses must convert their genomes (+ssRNA) into double-stranded DNA (dsDNA) using reverse transcriptase (RNA-dependent DNA polymerase activity) before integration into the host genome can occur. - Once integrated, the viral genome is replicated along with the host cell's own DNA as a lysogenic provirus. Consequently, the original cell containing the integrated viral genome will divide and produce descendants that are also infected.

Signal sequences

Signal sequences are short amino acid sequences typically located at the N-terminus of a polypeptide that are used by both eukaryotic and prokaryotic cells to direct proteins to precise destinations within the cell. Educational objective: Prokaryotic cells lack membrane-bound organelles and utilize specialized channels in the plasma membrane to secrete proteins. In contrast, eukaryotic cells contain membrane-bound organelles; the rough ER and Golgi body are involved in eukaryotic protein secretion.

Viruses with single-stranded RNA genomes - can directly translate their genetic material into viral proteins upon infection of a host cell.

Specifically, some viruses with single-stranded RNA genomes can directly translate their genetic material into viral proteins upon infection of a host cell. The virus shown in the diagram possesses a genome that can be immediately translated into protein following infection of the Escherichia coli cell. Therefore, this virus must have a single-stranded RNA genome, which can be detected with northern blot analysis.

Microtubles (a type of cytoskeleton in cells) - originate near the nucleus on small organelles called centrioles and radiate out toward the plasma membrane.

The cytoskeleton is an intracellular scaffolding network of fibers that are interspersed throughout the cytoplasm. It functions to give the cell its shape, support cellular motility, and help organize intracellular components. The three major cytoskeletal components are actin filaments (ie, microfilaments), intermediate filaments, and microtubules. Microtubules are composed of alternating α- and β-tubulin subunits that assemble into hollow tubes. They are involved in various forms of movement within the cell; microtubules form the mitotic spindle during cell division and are essential for cell motility as they form the core of cilia and flagella. Microtubules also facilitate transport of vesicles such as endosomes and other organelles from one location in the cell to another. The microtubules involved in intracellular transport originate near the nucleus on small organelles called centrioles and radiate out toward the plasma membrane. Endosomes move along microtubule tracks toward the nucleus. They enter the cell at the plasma membrane moving toward the centrioles near the nucleus.

The endosomal pathway - retrograde through secretory pathway OR - get degraded by lysosome

The endosomal pathway begins at endocytosis - where, following internalization of extracellular materials into vesicles, the vesicles containing these materials mature to early endosomes, late endosomes, and finally, lysosomes. The lysosome is a membrane-enclosed organelle that serves as the "digestive system" of the cell; it contains an acidic environment (pH ≈ 4.5) and various hydrolytic enzymes that facilitate the degradation of various biomolecules (eg, proteins, carbohydrates, nucleic acids, lipids). Normally, endosomes can participate in retrograde trafficking, which refers to the reversal of a pathway in the context of cellular trafficking. In this case, retrograde trafficking leads to endosomes producing vesicles that fuse with the Golgi apparatus. This allows the cargo within the vesicles to enter the secretory pathway and be expelled from the cell by exocytosis (ie, bypassing degradation by the lysosome). Viruses inhibits retrograde trafficking of the endosomal pathway (cannot get through). - Therefore, virial particles that fail to escape acidified endosomes cannot enter the Golgi or other secretory pathway organelles to undergo exocytosis - The only other available fate is the lysosome, where the viral particles will be degraded.

Under anaerobic conditions, - ATP synthase is not active in Euks - ATP synthase is active in Proks

The enzyme ATP synthase harnesses the potential energy of the ETC proton gradient to generate ATP from ADP and inorganic phosphate. Although ATP synthase does not directly need O2 to generate ATP, the formation of the proton gradient by which it functions is oxygen-dependent in Euks but not in Proks. Consequently, under anaerobic conditions, ATP synthase is not active in Euks but is active in Proks

Experiment - To determine if a virus is enveloped or non-enveloped

To determine if a virus is enveloped or non-enveloped - they are exposed to fluorescent antibodies designed to bind viral capsid proteins directly. If the antibodies were able to bind directly to the capsid proteins of both viruses, it can be determined that they are non-enveloped viruses (ie, they do not have a phospholipid bilayer enveloping the capsid). The absence of fluorescence indicates that the viruses are enveloped viruses, meaning that their capsid proteins are covered by a protective phospholipid bilayer and cannot be bound by the antibody used by the researchers. Educational objective: All viruses contain a protective protein coat known as the capsid. Viruses that contain only a capsid as an outer layer are known as non-enveloped or naked viruses, and are able to survive in harsh conditions. Viruses with a phospholipid bilayer surrounding the viral capsid are referred to as enveloped viruses; these are more susceptible to changes in environmental conditions.

VIRUSES

VIRUSES

Viral load, ddDNA and - Their viral genes are transcribed into positive-sense, single-stranded mRNA (+ssRNA) in the nucleus by the eukaryotic DNA-dependent RNA polymerase, also known as Pol II.

Viral load is measured by the total quantity of viral genetic material inside an organism. Once inside a host, viruses rely on cellular (host) and/or viral polymerases to replicate their genomes and produce mRNAs that can be used for viral protein synthesis. double-stranded DNA viruses have double-stranded genomes that are similar to the host cell's genome; - as a result, they can directly utilize host enzymes. Their viral genes are transcribed into positive-sense, single-stranded mRNA (+ssRNA) in the nucleus by the eukaryotic DNA-dependent RNA polymerase, also known as Pol II. This polymerase produces positive-sense mRNA that codes for viral proteins, which are subsequently detected by the immune system. Inhibition of Pol II in mice infected with HBV would prevent the virus from utilizing the host enzymes, therefore stopping production of viral mRNAs and proteins. Consequently, there is a decrease in viral load. Because the numbers of cells presenting viral particles follow patterns similar to the amount of viral load in the blood, there will also be a decrease in antigen-presenting cells displaying HBV fragments as a consequence of the treatment with the antiviral drugs

fluid mosaic model,

fluid mosaic model, - Describes the membrane of an animal cell in which transmembrane proteins (membrane proteins) and other components reside in a fluid bilayer composed largely of phospholipids. The cell membrane is said to be fluid as its various nonphospholipid components are able to migrate *laterally* through the entire phospholipid-rich surface of the cell in any direction. These other important components include cholesterol, glycoproteins, and glycolipids (proteins and lipids that have been modified with carbohydrates).