• Mader 11

Chapter 20

• Viruses, Bacteria, and Archaea

• Viruses• -Are associated with a number of plant, animal, and human diseases• -Can only reproduce by using the metabolic machinery of the host cell• -Are noncellular• -May have a DNA or RNA genome• In 1884, Pasteur suspected something smaller than bacteria caused rabies;

he chose a Latin term for “poison”• In 1892, Russian biologist Dimitri Ivanowsky, working with the tobacco

mosaic virus, confirmed Pasteur’s hypothesis that an infectious agent smaller than a bacteria existed

• With the invention of the electron microscope, these infectious agents could be seen for the first time

• The classification of viruses has two parts• Part one sorts viruses based on their type of nucleic acid, including whether

they are single-stranded or double-stranded• Part two classified viruses similar to the Linnaean classification system:

order, family, genus, species• Viruses range in size from 10 to 400nm• Viruses are categorized by:

• -Their size and shape• -The type of nucleic acid• -The presence or absence of an outer envelope• All viruses have at least two parts: an outer capsid, composed of protein

subunits and an inner core, containing either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid), but not both

• The viral genome at most has several hundred genes; a human cell, in comparison, contains thousands of genes

• The viral envelope is usually partly host plasma membrane with viral glycoprotein spikes

• Viral particles have proteins, especially enzymes (e.g., polymerases), to produce viral DNA or RNA

• Not all viruses have an envelope; such viruses are called naked viruses• Viruses are obligate intracellular parasites that cannot multiply outside a

living cell; they must infect a living cell in order to reproduce• Animal viruses in laboratories are raised in live chick embryos or in cell

tissue culture• Viruses infect all sorts of cells, from bacteria to human cells, but they are

host specific

• The tobacco mosaic virus infects only certain plants• The rabies virus infects only mammals• The AIDS virus, HIV, infects only certain human blood cells• Some believe that viruses originated from the very cells that they infect• For example, viral nucleic acids originated from the host cell genome• Therefore, viruses evolved after cells came into existence; new viruses are

probably evolving now• Others suggest that viruses arose before the three domains• Viruses often mutate, therefore, it is correct to say they evolve• Those that mutate are troublesome; a vaccine effective today may not be

effective tomorrow• Influenza (flu) viruses mutate regularly• Viruses gain entry into and are specific to a particular host cell because

portions of the capsid (or spikes of the envelope) adhere to specific receptor sites on the host cell surface

• Viral nucleic acid then enters a cell, where viral genome codes for production of protein units in the capsid

• A virus may have genes for a few special enzymes needed for the virus to reproduce and exit from a host cell

• A virus relies on host cell enzymes, ribosomes, transfer RNA, and ATP for its own replication

• Bacteriophages (phages) are viruses that parasitize bacteria• The lytic cycle is a bacteriophage’s “life” cycle consisting of five stages• 1. During attachment, portions of the capsid bind with receptors on the

bacterial cell wall• 2. During penetration, a viral enzyme digests part of a cell wall; the viral

DNA is injected into a bacterial cell• 3. Biosynthesis involves synthesis of viral components and begins after the

virus brings about inactivation of host genes not necessary to viral replication

• 4. During maturation, viral DNA and capsids are assembled to produce several hundred viral particles and lysozyme, coded by the virus, is produced

• 5. When lysozyme disrupts the cell wall, release of the viral particles occurs and the bacterial cell dies

• With the lysogenic cycle, the virus incorporates its DNA into the bacterium but only later is phage produced

• Following attachment and penetration, viral DNA becomes integrated into bacterial DNA with no destruction of the host DNA

• At this point, the phage is latent and the viral DNA is called a prophage• The prophage is replicated along with the host DNA; all subsequent cells

(lysogenic cells) carry a copy • Certain environmental factors (e.g., ultraviolet radiation) induce prophage to

enter the biosynthesis stage of the lytic cycle, followed by maturation and release

• Animal viruses replicate similarly to bacteriaphages, but there are modifications

• -If the virus has an envelope, glycoprotein spikes allow it to adhere to plasma membrane receptors

• -The virus genome covered by the capsid penetrates the host cell• -Once inside, the virus is uncoated as the envelope and capsid are removed• -Free of its covering, the viral genome (DNA or RNA) proceeds with

biosynthesis• -Newly assembled viral particles are released by budding• -Components of viral envelopes (i.e., lipids, proteins, and carbohydrates)

are obtained from the plasma or nuclear membrane of the host cell as the viruses leave

• Retroviruses are RNA animal viruses that have a DNA stage

• -Retroviruses contain the enzyme reverse transcriptase that uses RNA as a template to produce cDNA a copy of the viral genome

• -Viral cDNA is integrated into host DNA and is replicated as host DNA replicates

• -Viral DNA is transcribed; new viruses are produced by biosynthesis and maturation; release is by budding

• Emerging viruses are new or previously uncommon illnesses that infect large number of individuals

• -In some cases of emerging diseases, the virus is simply transported from one location to another; e.g., West Nile virus and severe acute respiratory syndrome (SARS)

• -The high mutation rate of viruses also causes infectious viruses to emerge e.g., AIDS and Ebola fever

• -Viruses can also move between different species• -A change in the mode of transmission is yet another way infectious viruses

could emerge• Viroids are naked strands of RNA, a dozen of which cause crop diseases• Prions (proteinaceous infectious particles) are newly discovered disease

agents that differ from viruses and bacteria

• Transmissible spongiform encephalopathies (TSE) are neurodegenerative diseases that destroy nerve tissue in the brain and they are untreatable and fatal

• Flu viruses have an H (hemagglutinin) spike that attaches to a cell receptor; there are 16 known types of H spikes and an N (neuraminidase) spike that attaches to host plasma membrane so viruses can exit the cell and there are nine known N spikes

• H5N1 (bird flu) gets its name from its variety of H5 spikes and its variety of N1 spikes

• Our immune system only recognizes a particular variety of H and N spikes it has been exposed to

• When a new flu virus arises and there is little or no immunity in the human population, a flu pandemic may occur

• Prokaryotes include the bacteria and archaea• They are fully functioning, single-celled organisms• They were discovered in the seventeenth century by Antonie van

Leeuwenhoek; they were thought to arise spontaneously from inanimate matter

• Around 1850, Pasteur devised an experiment showing that bacteria present in air contaminated the media

• A single spoonful of soil contains 1010 prokaryotes; these are the most numerous life forms

• Prokaryotes range in size from 1-10 um in length and 0.7-1.5 um in width• Prokaryote means before a nucleus—their cells lack a eukaryotic nucleus• Prokaryotic fossils date back as far as 3.5-3.8 billion years ago• Fossils indicate prokaryotes were alone on earth for 2 billion years; they

evolved very diverse metabolic capabilities• Outside the plasma membrane of most cells is a rigid cell wall that keeps the

cell from bursting or collapsing due to osmotic changes by peptidoglycan, a complex molecule containing a unique amino disaccharide and peptide fragments

• Some prokaryotes move by means of flagella; flagellum is capable of 360 degree rotation which causes the cell to spin and move forward

• Many prokaryotes adhere to surfaces by means of fimbriae, short hairlike filaments extending from the surface

• Prokaryotic cells lack the membranous organelles of eukaryotic cells• Various metabolic pathways are located on the plasma membrane• A nucleoid is a dense area in prokaryotes where the chromosome is

located; it is a single circular strand of DNA

• Plasmids are accessory rings of DNA found in some prokaryotes; they can be extracted and used as vectors to carry foreign DNA into bacteria during genetic engineering procedures

• Binary fission is the splitting of a parent cell into two daughter cells; it is asexual reproduction

• Prokaryotes are haploid; mutations are therefore immediately subjected to natural selection

• In bacteria genetic recombination can occur in three ways:• 1. Conjugation occurs when a bacterium passes DNA to a second bacterium

through a tube (sex pilus) that temporarily joins the two cells• 2. Transformation involves bacteria taking up free pieces of DNA secreted

by live bacteria or released by dead bacteria• 3. In transduction, bacteriophages transfer portions of bacterial DNA from

one cell to another• Bacteria are the most common type of prokaryote• The Gram stain procedure (developed in the late 1880s by Hans Christian

Gram) differentiates bacteria• -Gram-positive bacteria stain purple, whereas Gram-negative bacteria stain

pink; difference is dependent on thick or thin peptidoglycin cell wall

• Bacteria and archaea have three basic shapes• 1. A spirillum is spiral-shaped• 2. A bacillus is an elongated or rod-shaped bacteria• 3. Coccus bacteria are spherical• Cocci and bacilli tend to form clusters and chains of a length typical of the

particular species.• Obligate anaerobes are unable to grow in the presence of O2; this includes

anaerobic bacteria that cause botulism, gas gangrene, and tetanus• Facultative anaerobes are able to grow in either the presence or absence of

gaseous O2

• Aerobic organisms (including animals and most prokaryotes) require a constant supply of O2 to carry out cellular respiration

• Photoautotrophs are photosynthetic and use light to assemble the organic molecules they require

• Chemoautotrophs make organic molecules by using energy derived from the oxidation of inorganic compounds in the environment

• Most free-living bacteria are chemoheterotrophs that take in pre-formed organic nutrients

• As aerobic saprotrophs, there is probably no natural organic molecule that cannot be broken down by some prokaryotic species

• Bacteria produce chemicals including ethyl alcohol, acetic acid, butyl alcohol, and acetones

• Bacteria action produces butter, cheese, sauerkraut, rubber, cotton, silk, coffee, and cocoa

• Antibiotics are produced by some bacteria• Mutualistic bacteria that live in the intestines of humans benefit from

undigested material and release vitamins K and B12, which we use to produce blood components

• Commensalistic bacteria live in or on organisms of other species and cause them no harm

• Parasitic bacteria are responsible for a wide variety of infectious plant, animal, and human diseases

• Parasitic bacteria that cause disease are called pathogens• Some bacteria form resistant endospores in response to unfavorable

environmental conditions• Endospore formation is not reproduction—it is a means of survival and

dispersal to new locations• Cyanobacteria are Gram-negative bacteria that photosynthesis in the same

manner as plants, and thus are responsible for introducing O2 into the primitive atmosphere

• Cyanobacteria were probably the first colonizers of land during evolution• Archaea are prokaryotes with molecular characteristics that distinguish them

from bacteria and eukaryotes; their rRNA base sequence is different from that in bacteria

• Archaea have unusual lipids in their plasma membranes that allow them to function at high temperatures; glycerol linked to hydrocarbons rather than fatty acids

• Cell walls of archaea do not contain peptidoglycan found in bacterial cell walls

• Methanogens live under anaerobic environments (e.g., marshes) where they produce methane

• -Methane is produced from hydrogen gas and carbon dioxide and is coupled to formation of ATP

• -Methane released to the atmosphere contributes to the greenhouse effect• -About 65% of the methane found in our atmosphere is produced by

methanogenic archaea• Halopiles require high salt concentrations (e.g., Great Salt Lake)• -Their proteins have unique chloride pumps that use pumps that use

halorhodopsin to synthesize ATP in the presence of light

• -They usually require 12-15% salt concentrations; the ocean is only 3.5% salt

• Thermoacidophiles live under hot, acidic environments (e.g., geysers)• -They survive best at temperatures above 80 degrees C; some survive

above boiling temperatures• -Metabolism of sulfides forms acidic sulfates; these bacteria grow best at pH

of 1 to 2• Archaea are found in all moderate environments as well as extreme

environments• Some archaea have symbiotic relationships with other organisms• Archaea may have a role in nutrient cycling