Viruses: Structure, Function, and Evolution

Structural Components of Viruses

• Capsid: Protein shell that encloses a viral genome; may be rod-shaped, polyhedral, or more complex in shape
• Viral envelopes: Membrane that cloaks the capsid that in turn encloses a viral genome

Obligate Intracellular Parasites

Viruses can only reproduce within host cells because they lack metabolic enzymes, ribosomes, and other equipment for making proteins.

• Identifying host cells: "Lock and key" fit between proteins on the outside of the virus and specific receptor molecules on the host's surface (which originally evolved for functions that benefit the host).

Bacterial Defenses Against Phages

While phages have the potential to wipe out a bacterial colony in just hours, bacteria have defenses against phages:

• Natural selection favors bacterial mutants with receptor sites that are no longer recognized by a particular type of phage
• Bacteria produce restriction enzymes that recognize and cut up foreign DNA, including certain phage DNA - their activity restricts the ability of the phage to infect the bacterium
• Chemical modifications to the bacteria's own DNA prevent its destruction by restriction enzymes

Lytic vs. Lysogenic Cycles

Lytic cycles: Destroys the host Lysogenic cycles: Phage genome replicates without destroying the host cells

Which viral genes are expressed during the prophage stage?

One of the viral genes codes for a protein that represses most other prophage genes.

As a result, the phage genome is largely silent.

Every time the host divides, it copies the phage DNA and passes the copies to daughter cells (thus propagating without killing the host cells on which they depend).

Reproductive Cycle of an Enveloped Virus

• Glycoproteins on the envelope bind to specific receptors on the host's membrane
• Envelope fuses with the host's membrane, transporting the capsid and the viral genome inside
• In the reproductive cycle of an enveloped virus with an RNA genome, viral glycoproteins for new envelopes are made by ribosomes bound to the ER of the host cell
• Viral glycoproteins are than glycosylated by cellular enzymes in the ER and Golgi apparatus
• These glycoproteins are transported to the cell surface, where they wrap themselves in membrane as they bud from the cell

Reproductive Cycle of an HIV Retrovirus

• After HIV enters the host cell, reverse transcriptase molecules are released into the cytoplasm and catalyze the synthesis of viral DNA
• Newly made viral DNA enters the cell's nucleus and is inserted as a permanent provirus into a chromosome
• Host's RNA polymerase transcribes the proviral DNA into RNA molecules that can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell

Characteristics of Viruses

• Use of genetic code
• Obligate intracellular parasites that cannot reproduce independently

Viruses do not fit our usual definition of life because:

• They can reproduce only within a host cell
• No ribosomes to make proteins
• Generally no source of energy

Evolution of Viruses

Most molecular biologists favor the hypothesis that the earliest viruses were naked bits of nucleic acids that passed between cells via injured cell surfaces.

Evolution of capsid genes may have facilitated the infection of undamaged cells.

Viral Infections and Disease

• Some viruses damage or kill cells by triggering the release of hydrolytic enzymes from lysosomes
• Some viruses cause the infected cell to produce toxins that lead to disease symptoms
• Other viruses have molecular components, such as envelope proteins, that are toxic

Emergence of New Viral Diseases

• Mutation of existing viruses is a major source of new viral diseases
• Viral disease can spread from a small, isolated population to become a widespread epidemic
• Spread of existing viruses from one host species to another

Transmission of Viral Diseases in Plants

• Horizontal: A plant is infected with the virus by an external source
• Vertical: A plant inherits a viral infection from a parent

Non-Replicating Protein as a Transmissible Pathogen

A prion is a misfolded form of a normal brain protein.

When the prion gets into a cell with the normal form of the protein, the prion can convert the normal protein to the prion version, creating a chain reaction that increases their numbers.

Viroids and Prions

Viroids: Circular RNA molecules that infect plants and disrupt their growth. Prions: Slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals. Prions propagate by converting normal proteins into the prion version.

Bacteriophages

Virus that infects bacteria; also called a phage

Tobacco Mosaic Virus

Helical capsid with the overall shape of a rigid rod

Adenoviruses

An icosahedral capsid with a glycoprotein spike at each vertex

Influenza Viruses

Outer envelope studded with glycoprotein spikes; genome consists of eight different RNA molecules, each wrapped in a helical capsid

Bacteriophage T4

Complex capsid consisting of an icosahedral head and a tail apparatus

Host Range

Limited range of host cells that each type of virus can infect

Lytic Cycle

Type of phage reproductive cycle resulting in the release of new phages by lysis (and death) of the host cell

Virulent Phage

Phage that reproduces only by a lytic cycle

Restriction Enzymes

An endonuclease (type of enzyme) that recognizes and cuts DNA molecules foreign to a bacterium (such as a phage genomes); enzyme cuts at specific nucleotide sequences (restriction sites)

Lysogenic Cycle

Type of phage reproductive cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage and does not kill the host

Temperate Phages

Phage that is capable of reproducing by either a lytic or lysogenic cycle

Prophage

Phage genome that has been inserted into a specific site on a bacterial chromosome

Retroviruses

RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses

Reverse Transcriptase

Enzyme encoded by certain viruses (retroviruses) that use RNA as a template for DNA synthesis

HIV

(Human immunodeficiency virus) infectious agent that causes AIDS; a retrovirus

AIDS

(Acquired immunodeficiency syndrome) symptoms and signs present during the late stages of HIV infection, defined by a specified reduction in the number of T cells and the appearance of characteristic secondary infections

Provirus

Viral genome that is permanently inserted into a host genome

Vaccine

Harmless variant or derivative of a pathogen that stimulates a host's immune system to mount defenses against the pathogen

Epidemics

General outbreak of a disease

Pandemic

Global epidemic

Prions

Infectious agent that is a misfolded version of a normal cellular protein; appear to increase in number by converting correctly folded versions of the protein to more....

Viroids

Plant pathogen consisting of a molecule of naked, circular RNA a few hundred nucleotides long

Mobile Genetic Elements

. a type of DNA that can move around within the genome:  plasmids, transposons and viruses. Transposons DNA segments that can move from one location to another within a cell's genome. Plasmids small, circular DNA molecules found in bacteria and in the unicellular eukaryotes called yeasts. Exist apart from the cell's genome and can replicate independently of genome and are occasionally transferred b/w cells.