Extracellular Components and Cell Walls

Viruses have diverse shapes determined by their nucleocapsid. These shapes can be helical, polyhedral, spherical, or complex.

A naked virus lacks an envelope, which is a lipid membrane surrounding the nucleocapsid. This can make them resistant to environmental factors.

An enveloped virus has a phospholipid bilayer envelope containing viral proteins taken from the host cell. This helps with protection and entry into new cells.

Budding is the process by which enveloped viruses exit host cells. They acquire a membrane from the host cell.

Some viruses can become dormant, or inactive, inside a host cell and avoid being detected. They later reactivate.

A large, strong protein forming fibrils by intertwining three polypeptide strands (triple helix). It's abundant in connective tissue and extracellular matrix.

Provides structural support and strength to connective tissues like tendons and ligaments, and is part of the extracellular matrix.

An insoluble fiber that links collagen to cell membranes via transmembrane proteins (integrins).

A network of protein filaments, not an organelle, found throughout the cell, providing structural support, and enabling movement.

Provides structural support for the cell and organelles. Maintains cell shape and internal organization.

Enables cell movement and internal transport (of organelles, vesicles).

The cytoskeleton isn't a fixed structure; it can assemble and disassemble as needed.

Forces from outside the cell are transmitted through cell surface proteins into the cell by cytoskeletal elements, even reaching the nucleus.

COVID-19, a coronavirus, uses endocytosis or receptor-mediated fusion to enter human cells, then replicates its RNA genome to create new viruses, which are released when the host cell bursts.

HIV, a retrovirus, converts its RNA genome into DNA, which is incorporated into the host cell's DNA. New viruses are then assembled and released from the host cell.

Viruses, like COVID-19, can enter host cells by endocytosis or receptor-mediated fusion.

Viral replication method where the virus immediately takes over the host cell's machinery to create new viruses, which burst out of the host cell, killing it.

Two main methods of viral genome reproduction inside a host cell are: Lytic Cycle and Lysogenic Cycle. In Lytic, the virus immediately replicates, and in Lysogenic, the viral genome integrates into the host cell's DNA.

Coronaviruses are enveloped RNA viruses. Their structure includes a prominent spike protein on the surface.

Retroviruses, like HIV, are enveloped RNA viruses with cone-shaped capsids and an enzyme called reverse transcriptase which converts RNA to DNA.

HIV targets T-helper cells in the human immune system for replication.

Facilitated diffusion relies on transport proteins, increasing the speed of substrate diffusion. However, since these transporters have a limited number, they reach a maximum rate, where all available proteins are occupied.

Active transport moves substances against their concentration gradient. This process requires metabolic energy, typically obtained from ATP breakdown.

Active transport can be driven by coupling the movement of a substance against its gradient with another substance moving down its gradient, releasing energy.

Insulin's presence increases the number of glucose transporters in the plasma membrane by promoting their movement from intracellular vesicles. This process enhances glucose uptake, especially after a meal.

After insulin levels drop, glucose transporters are removed from the plasma membrane by endocytosis. They are packaged into vesicles and recycled back to the surface when insulin levels rise again.

After digestion, glucose needs to move from the intestinal lumen into epithelial cells against its concentration gradient, requiring energy. This energy is provided by simultaneous Na+ transport down its electrochemical gradient.

In the nephrons of kidneys, glucose is filtered from blood. To prevent loss, glucose is reabsorbed from the renal filtrate with the help of Na+ dependent glucose cotransporters on kidney epithelial cells.

Influx refers to the flow of particles into a cell or compartment.

Efflux refers to the flow of particles out of a cell or compartment.

Facilitated diffusion uses transport proteins to move molecules down their concentration gradient (no energy required). Active transport moves molecules against their concentration gradient, requiring energy.

Simple diffusion is the passive movement of molecules across a membrane based on their size and hydrophobicity/hydrophilicity.

Vesicles are small membrane sacs that transport large molecules (proteins, polysaccharides) across cell membranes.

Endocytosis is the process of cells engulfing particles by forming vesicles from the plasma membrane.

Phagocytosis is the engulfment of solid particles by cells, like bacteria or debris.

Pinocytosis is the engulfment of liquid droplets by cells.

N.equitans is a hyperthermophile that is a parasite of another hyperthermophile. It lacks genes for metabolism, relying on its host for its metabolic functions.

One theory suggests viruses may have evolved from intra-parasitic bacteria that lost their ability to live independently, relying on hosts for reproduction and losing more and more functions, resulting in smaller genomes.

Some bacteriophages use a modified base, diaminopurine (Z), instead of adenine in their DNA. This makes the DNA more heat-stable and protects against host attack.

Structural similarities in viruses might result from convergent evolution, where different viruses independently adapt similar traits in similar environments or under similar pressures.

Viruses evolve at a significantly faster rate than most organisms due to factors like high mutation rates, genetic exchange, and short generation times.

RNA viruses often have high mutation rates because they use error-prone enzymes like reverse transcriptase, which are less accurate than DNA polymerases.

HIV, a retrovirus, uses enzymes like reverse transcriptase for DNA synthesis and integrase for integration into the host genome. Its genome contains genes for structural proteins, replication enzymes, and envelope proteins.

HIV has the highest known mutation rate among viruses, driven by error-prone reverse transcriptase and host enzymes like cytidine deaminase, which can introduce mutations.

The spike proteins on SARS-CoV-2 are crucial for recognizing host cells and fusing with the host cell membrane.

SARS-CoV-2, due to rapid replication and mutations, generates new variants through changes in its RNA sequence. Some variants can be more transmissible or evade immune responses.

Influenza virus uses enzymes like RNA-replicase (RNA-dependent polymerase) to make more RNA strands and RNA-endonuclease to cut RNA. RNA polymerase lacks proofreading, leading to high mutation rates.

Influenza viruses undergo antigenic drift, subtle changes in their surface antigens (HA and NA), due to mutations. This can diminish host immunity, leading to reinfection.

Antigenic shift in influenza occurs when segments of RNA genomes from different strains reassort within a host, creating a new virus with unique surface antigens.

A cladogram, based on similarities in RNA genome sequences, can be used to classify and understand the evolutionary relationships between different viruses.