MSCI345 Viruses & Prokaryotes

cell

ALL life on earth evolved from one, simple, ancestral “ “ and that many of the features shared by living organisms today were inherited from that ancient ancestor.

Evidence of a singular ancestor

all known life

* shares the same basic genetic code


* similar bilipid cell membrane

abiotic chemical evolution

“ “ early in earth’s history that eventually gave rise to some type of self-replicating molecules (very likely some form of RNA) as well as all four of the major classes of carbon-based molecules found in living organisms today

four of the major classes of carbon-based molecules

* lipids
* carbohydrates
* proteins
* nucleic acids

reproduce, characteristics

If you have something that can “ “ itself and pass its “ “ to its descendants, especially if that process is imperfect (so there is some random variation thrown in), then you have everything needed for biological evolution to take off. 

4\.5 billion

The best evidence we have available today indicates that the Earth is about “ “ years old

3\.8 billion

The oceans could not have formed until the surface of the young Earth cooled below the boiling point of water, probably sometime about “ “ years ago.

3.5 billion

There is pretty clear evidence that photosynthetic bacterial cells were living in earth’s shallow ocean waters at least “ “ ago.

Stromatolites

We know this because some types of cyanobacteria living in shallow tropical seas today form distinctive, layered, mound-like structures called **“ “** , and fossils of them have been found in rocks dated to 3.5 billion years ago.

3\.8 and 3.5 billion

It looks like life probably started in earth’s ocean sometime between about “ “ years ago.

DNA sequencing, molecular biology, and other techniques

Our understanding of the early evolution of life on Earth is itself evolving rapidly as new evidence pours in, largely due to recent developments in “ “

bacteria

The earliest life forms on Earth were probably more similar to modern-day **“ “** than to any other living life forms, so we can think of the base or trunk of the Tree of Life as being some sort of “ “-like cell.

3\.2 and 2.5 billion, Archaea

 A major split occurred somewhere between about “ “ years ago, when a taxon we now call **“ “** split off from the more ancient lineage of bacteria-like organisms.

Prokaryote

In particular, they tend to be single celled with no nucleus or other membrane-bound organelles within the cell, and their DNA tends to be in a single loop with no histone proteins.

Eukaryote

These organisms have cells with features not found in prokaryotes, including a nucleus and other membrane-bound organelles, like mitochondria, and genetic material composed of DNA wrapped around histone proteins to form a material called chromatin.

1.6 and 2.1 billion

The best estimates today put the origin of eukaryotes at sometime between about ” “ years ago.

mutualistic symbiosis

It now looks like eukaryotes arose from a “ “ between an ancient archaeal cell and one or more bacterial cells.

proteobacterium

Based on lots of molecular and other evidence, here’s what we think probably happened: Some predatory archaeal cell engulfed, but did not successfully digest, a bacterial cell, most likely from a lineage of bacteria known as “ “.

cyanobacterium

Subsequently, some descendents of this primitive eukaryotic cell, complete with their proteobacteria-derived mitochondria, apparently engulfed, but failed to properly digest, a photosynthetic “ “. This seems to be the origin of the photosynthetic chloroplasts found in today’s green plants and algae.

paraphyletic

For the purposes of this class, you do not need to know whether there are two or three domains. However, you should know what the terms Bacteria, Archaea, Eukaryote, and Prokaryote refer to, and you should recognize that the terms Prokaryote, Bacteria, and Archaea are almost always used in their “ “sense.

100 billion, 10 billion

In fact, it turns out that a single 1-liter bottle of surface seawater typically contains about “ “ viruses and about “ “ prokaryotes

underestimated

Initial evidence strongly suggests that we have grossly “ “ the ecological importance of marine viruses and prokaryotes just as we have, until recently, “ “ their abundance and diversity.

genetic material,

capsid

Viruses typically consist of a small amount of **“ “** (DNA or RNA) encased in a protein shell or coat called a **“ “**.

50 nm

Viruses are extremely small, averaging about “ “, or 0.05 μm. (That’s about 1/1000th of the diameter of a human hair.)

Life-like properties of Viruses

* They contain genetic material (DNA or RNA)
* They can reproduce. (Sort-of; more on this in a moment.)
* They evolve (witness the rapid evolution of new COVID variants!)
* Like predators or parasites, they have strong ecological interactions with living organisms.

Reasons why viruses are considered non-living

* They cannot reproduce by themselves. To reproduce, they must infect a host cell and hijack its gene-replicating and protein-making abilities to make copies of the virus’ genetic material and capsid proteins, which then self-assemble into new virus particles within the host cell.
* They have no metabolism -- they don’t eat, breathe, or do any of the metabolic chemical reactions (like glycolysis, etc.) we normally associate with being alive.

bacteriophages

The majority of marine viruses appear to be “ “ (i.e., they attack bacteria as their host cells).

dissolved organic matter (DOM)

molecular “gunk” released by bacterial cells bursting; an important source of nutrients for other microorganisms and for some multicellular algae, including the giant kelp that creates underwater forests in the Monterey area and beyond.

1 micrometer

Most prokaryotes are very small (but not quite as small as viruses) averaging on the order of “ “ in diameter.

bilipid layer, cell wall

They have one cell membrane composed of a “ “, and they usually have a “ “outside the cell membrane that may be made of several different materials, depending on the particular prokaryote group.

Characteristics of Prokaryotes

* They have no nucleus or other internal membrane-bound organelles.
* They have as their genetic material a single loop of DNA without histone proteins.

Proteobacteria

* Many species are important as disease-causing bacteria on land and in the sea.
* Many species are important as nitrogen fixers. Nitrogen fixers convert atmospheric nitrogen (N2), which is very stable and nearly impossible for other organisms to break down, into other nitrogen-containing molecules that are more easily accessible, allowing other organisms to build proteins and other nitrogen-containing molecules.
* The mitochondria found in eukaryotic cells are genetically very closely related to proteobacteria and share other biomolecular characteristics with them. Therefore, we think mitochondria are probably descended from an ancient proteobacterium that was engulfed, but not digested, by an archaeal cell that thereby became the ancestor of all eukaryotic cells.

Cyanobacteria

* Formerly known as blue-green algae.
* Probably the first photoautotrophs on Earth. Still extremely important as primary producers.


* Cyanobacteria are also important as nitrogen fixers, which take inorganic nitrogen (another super-stable molecule) and convert it into an accessible form that other cells can use.
* They are responsible for some (but not all) red tides and harmful algal blooms (HABs).

Photosynthesis’ advantages

1. It stores solar energy in chemical bonds, thereby making that energy accessible for powering biochemical reactions.
2. It takes carbon atoms from carbon dioxide molecules, which are too stable for most organisms (including us) to break down, and makes those carbon atoms available in glucose, where they can be used by other organisms (like us) to build all of the important carbon-based molecules that support life on Earth.
3. It creates oxygen as a byproduct, which many types of organisms (including humans) have come to depend on for survival.

chloroplast

today’s plants and algae are probably descended from an early eukaryotic cell that engulfed (but did not successfully digest) a cyanobacterial cell, in much the same way as eukaryotes probably arose from an archeal cell that engulfed but did not digest, and proteobacterium. Evidence a “ “ is present in photosynthetic algae and plants

Decay bacteria

* Help to break down dead organisms.
* Important in nutrient cycling
* Practical applications for cleaning up oil spills, since some of them can “feed” on oil for energy.

Disease-causing bacteria

* Many diseases of corals, marine mammals, and other marine organisms are associated with bacteria that can survive in seawater and be transferred to hosts as plankton.

Beneficial endosymbionts

* Most marine (and terrestrial) animals have a unique microbiome of bacteria living in/on them, including the usually beneficial (indeed essential) bacteria in their gut that help with digestion.
* Bioluminescent animals, such as squid, fish, jellyfish, and many other animals in the ocean (and on land) rely on bioluminsescent bacteria to produce the light in their **photophores** (light producing organs).
* Some deep-sea animals, such as the deep-sea hydrothermal vent tube worms in the group Pogonophora, have **chemoautotrophic** forms of symbiotic bacteria that provide them with energy in places where there isn’t enough light for photosynthesis.
* Some organisms use them for defensive **toxin production.** For example, bacteria are the source of the deadly tetrodotoxin, or TTX, found in fugu/pufferfish, in the blue-ringed octopus, and in some of our local newts.

extreme

Archaea (as a group distinct from other bacteria) were first discovered by humans in “ “environments like hot springs, and for a long time they were thought to be restricted to otherwise inhospitable environments such as very hot, very salty, or very oxygen-poor places.