Biodiversity - Bio 11

Virus:

An infectious agent that replicates only inside the living cells of an organism

Structural Diversity:

In multicellular organisms is quite often obvious, and can be seen with the naked eye. Ex. a maple tree has a very different structure than a salamander

Also prevalent at a microscopic level in both multicellular and unicellular microscopic organisms

What are viruses classified as:

Classified by their capsid - the protein coating that surround their genetic

• Viruses are not alive

• Contain genetic material and reproduce

What are viruses?

A structure that contains strands of DNA or RNA surrounded by a protective protein coat and not able to live independently outside of host cells.

• Why viruses invade a host, and to be able to reproduce and survive with the aid of host cell’s organelles

What do viruses do outside of host cells?

• Considered dormant

• Neither eukaryote or prokaryote

• Don’t contain cytoplasm, membrane bound organelles, or cell membranes (why not considered living)

How do viruses affect living organisms?

• Causes diseases in plants and animals

• Ex of viruses in humans are polio, HIV, COVID19, and H1N1

Vaccinations:

• Most people have been vaccinated against polio, and each year against the seasonal flu virus

• Some viruses have yet to have a vaccine developed, HIV

The Capsid:

• Scientists will typically classify viruses in a category of their own, and will most often use size and shape capsid to classify it

• Capsid is outer protein layer that surrounds the genetic material of the virus

Common shapes of viruses:

1. Helical - Tobacco Mosaic Virus

2. Polyhedral - Adenovirus

3. Spherical - Influenza virus

4. Complex - Bacteriophage (typical ex people picture)

Reproduction (Virus):

• Don’t reproduce through mitosis or meiosis like eukaryotic or prokaryotic cells.

• Undergo replication (copied and new viruses produced)

• To occur, viruses must take advantage of host cell and typically end up producing many copies of themselves

• Replication follows one of two possibilities, lytic cycle or lysogenic cycle

Lytic Cycle:

Replication process in viruses in which the virus’s genetic material uses the copying machinery of the host cell to make new viruses

First step of Lytic Cycle (Attachment and entrance):

• Chemically recognizes a host cell, attaches to it and enters.

• Either a whole virus or only its genetic material enters the cell

Second step of the Lytic Cycle (Synthesis):

• Synthesis of protein and nucleic acids

• Makes the host cell make new virus “parts”

Third step of the Lytic Cycle (Assembly):

• Assembly of units

• Newly made virus parts are put together to form new virus particles

Fourth step of the Lytic Cycle (Release):

• Release of new viruses

• Host cell dies (called lysis)

Lysogenic Cycle:

Replication process in viruses, in which the viral DNA enters the host cell’s chromosomes;

• It may remain dormant and later activate and instruct the host cell to produce more viruses.

• When virus is reactivated at a later time, LYTIC cycle will resume

Provirus:

• As Lysogenic cycle takes place the viral DNA has become part of the host chromosome

• If occurs the infected cell has viral genes permanently

• host chromosome is referred to as a provirus

• Cell can still reproduce through mitosis, daughter cells will contain the provirus

Can invade a cell but does not kill it. When the virus is activated the provirus will leave the host chromosome and continue in the lytic cycle

Patterns in Diseases:

Replication patterns of viruses help to explain the patterns of some diseases

• Herpes simplex virus causes cold sores in humans which may appear and disappear on the skin of infected people throughout their lifetime

• Sores appear when the cycle destroys cells (lytic cycle)

• Sores disappear when the virus is in its provirus stage (lysogenic cycle)

Ex. HIV may remain dormant in affected humans for years showing no signs of infection, must be in lysogenic cycle and continuing to produce more cells containing provirus through mitosis

Prokaryotes:

Single-celled organisms from the domains Bacteria and Archaea that lacks a nucleus and membrane-bound organelles.

How many domains do Prokaryotes represent?

• Two out of three domains (bacteria and archaea)

• Both cases the kingdom name is the same as the domain name

• The fact that they are classified in different domains implies that these two types of unicellular organisms are vastly different ex. apple tree and lion from same domain

Morphology:

The most common forms in both bacteria and archaea are spheres and rods

1. Spherical shape known as cocci (singular coccus)

2. Rod shape is known as bacilli (singular bacillus)

3. Spiral shape, spirilla (singular spirillum)

Aggregation:

Though all prokaryotes are unicellular, both bacteria and archaea domains contain species that form aggregations which are clusters of individual cells grouped together

• A type of bacteria streptococcus, are found in chains which are made up of linked individual bacteria cells that are cocci

• A type of bacteria, streptobacillus, are found in chains that are made up of linked individual bacteria cells that are bacilli

Nutrition:

The cells in the Bacteria and Archaea domains obtain their energy through a variety of methods.

• Some will perform photosynthesis while other will consume other organisms.

• Some are able to obtain energy from various inorganic compounds such as hydrogen sulfide or iron

What is one specific method of metabolism unique to the Archaea domain?

Methanogenesis - category of metabolism that refers to biological or chemical process that produces methane as a by-product.

• It is a anaerobic (lack oxygen).

• Often one of the final stages of decomposition

• Archaea that perform methanogenesis are commonly found in the digestive tract of cattle, which is part of the reason beef and dairy industries are often blamed from playing a role in climate change

Methane (CH4):

is a simple organic compound that can be used as a fuel and also acts as a potent greenhouse gas.

What is one specific method unique to the Bacteria domain?

Photosynthesis is the method unique to bacteria.

• Most common type of bacteria that performs it is called cyanobacteria

• Abundant in both fresh water and salt water and are believed to account for much of the atmospheric oxygen on Earth

Habitat:

Due to the diversity of ways in which bacteria and archaea are able to obtain nutrients, there organisms are able to occupy a diverse array of habitats.

• Both archaea and bacteria occupy environments with oxygen (aerobic) and without (anaerobic)

• Ex. Methanogenic bacteria are abundant in the anaerobic depths of landfill sites, the guts of cattle, and sediments of swamps

• Ex. Humans, anaerobic bacteria are found in the human gut

How may Archaea and Bacteria differ in their ability to tolerate extreme environmental conditions?

• Many Archaea are considered extremophiles due to their ability to live in habitats characterized by extreme conditions.

• As our understanding has developed, it has influenced the belief of extraterrestrial life due to ability to withstand extreme conditions

• Many Bacteria are considered mesophiles because they occupy habitats that are characterized by moderate environmental conditions

Thermophile (heat lover):

The most heat-tolerant species known is the genus Methanopyrus, live near deep sea vents in temps as high as 120^oC.

Thermophile (Habitat):

Deep Sea Vents and Hot Springs

• Extreme temps over 100^oC

• Archaea that live around deep sea vents no only live with extreme temps, but in absence of sunlight

• Hot springs in Yellowstone National Park in U.S. is home to several different species of Archaea.

Acidophile (acid lover):

Picrophilus can live at a pH of 0, which is the acidity of car battery acid

Acidophile (Habitat):

Volcanic Crater Lakes and Mine Drainage Lakes

• Extremely acidic, pH of less than 3

• Sulfur from geothermal activity creates the acidic conditions of lakes in the craters of volcanoes

• Mine drainage lakes are human-made, result of mining operations

Halophile (salt lover):

When the concentration of salt in water exceeds 20% only halophilic archaea, such as Habcoccus, can thrive. Some live in concentrations as high as 37% salt.

Halophile (Habitat):

Salt Lakes and Inland Seas

• Salt lakes like Great Salt Lake, and inland seas like the Dead Sea can have concentrations of salt higher than 20%

• Dead Sea which has a high evaporation rate has a salt concentration of 35%

• Ocean water has a salt concentration of about 3.5%

Reproduction (Bacteria and Archaea):

Genetic material that is contained in prokaryotes is found in a single chromosome within the cell.

• Do not have nuclei so cannot reproduce via mitosis or meiosis rather they reproduce through a form of binary fission

• As cell grows it makes a copy of its original single chromosome, when the cell reaches a certain size it elongates and separates the two chromosomes within the cell then will build a partition between them call a septum

• After septum formed, cell bacteria and archaea are able to exchange DNA by conjugation

Conjugation:

Process produces cells with new genetic combinations, and thereby increases the diversity with the population, potentially adding new traits

• One cell links to another through a bridging structure and transfers all or part of its chromosome to the other cell. The new cell will then undergo binary fission to produce more cells with the same genetic make-up

Plasmids:

In most bacteria and archaea, the chromosome is not the only part of the cell that contains genes. Plasmids are small loops of DNA that are separate from the main chromosome and that contain genes

• Genes are different from those found in the chromosome

• Plasmids can split from the chromosome and rejoin it

• Plasmids may be transferred from one cell to another during conjugation, making them an important part of genetic recombination in prokaryotes

Endospores:

When environmental conditions threaten survival some species of bacteria can form endospores. They are hard walled structures that protect and store the organism’s genetic material.

• Endospores are resistant to high temperatures, drying out, freezing, radiation, and toxic chemicals

• When suitable conditions return, the endospore germinates back into an active bacterium

• Right now, endospores have not been observed in ARCHAEA