August 31: Kinds of Living Things - Bacteria, Archaea, Plants, Algae, Fungi, Animals   First Lecture: I am revising my lectures to fit this year's textbook Many of the web pages will be changed from what they are now. The ones now posted are based on a previous textbook . All the same topics will be covered, but which ones are covered first, etc. will sometimes be different. For example, an entirely new lecture on "the scientific method" will be added, and given on October 19th! Therefore, wait until then to worry about what our textbook says on pages 3 to 5. ************************************************************************************ What are the different kinds of living things?

Bacteria	Almost everything else
"Procaryotes"	"Eucaryotes"
bacteria	Animals
blue-green algae	Plants
	Fungi (mushrooms, yeasts)
	Algae
	Green Algae
	Brown Algae
	Red Algae
	Ciliates, etc.

 

The differences between bacteria and "real" plants are much more fundamental than the differences between humans and oak trees, or kelp, or mushrooms! Bacteria used to be considered just a kind of small plant; and Blue-Green Algae likewise. But really, they are VERY much simpler. Procaryotes    Bacteria (of which there are many sub-groups)    Blue-Green Algae    (which basically are one kind of photosynthetic bacteria) Have no nuclei. DNA genetic material is free in the cytoplasm. DNA is not bound to histone proteins. Have a plasma membrane around their cytoplasm. Most bacteria also have a cell wall; certain kinds don't. Cell walls are outside the cell, and made of sugars etc. Membranes are the cell's surface, and made of lipids (fats). Don't confuse cell walls with membranes. also remember that the "plasma membrane" is the membrane right at the outer edge of the cytoplasm. Procaryotes have a special ability "chemiosmosis" which you will learn about later. They use this to convert some kinds of chemical energy into a more useful form of chemical energy, by pumping hydrogen ions across their plasma membrane This discovery won the Nobel Prize, not too long ago. Chemiosmosis will be covered in a future lecture. Eucaryotes:    Animals    Plants    Fungi    Green Algae    Brown Algae    Red Algae    Ciliates,       etc. Similarities: the surface layer is the plasma membrane; and plant cells and fungi cells have cell walls. Differences: (there are many more than just these) DNA is enclosed in a nucleus (the surface of this nucleus is two layers of membrane) DNA is bound to a special kind of proteins, called "histones". The nucleus is one of several "organelles", each having its own kinds of membranes. The endoplasmic reticulum is one of these organelles. Two especially interesting kinds of organelle are . Chloroplasts (in plants and algae; not in animals) Mitochondria (in plants, and also in animals) Their function is to handle energy transfer, including photosynthesis in the case of chloroplasts. They use chemiosmosis for energy transfer. These organelles have seveal layers of membrane, two layers in mitochondria and three layers in chloroplasts. These organelles also contain DNA, with their own genes! They also grow and divide inside cells as if they were themselves separate little cells. (which they almost are!) Mitochondria evolved from symbiotic bacteria. Chloroplasts evolved from symbiotic blue green algae. About symbiosis, and symbiotic plants, (and other symbiotic organisms) ("symbiotic" = "commensal") Corals are a kind of animal, but inside the cytoplasm of each cell of all (healthy) corals live symbiotic green algae. The coral animals gets some of their oxygen, and vitamins, from these plant cells living in their cytoplasm. Corals will die in the dark; or if something kills their algae. Many kinds of sponges have symbiotic algae, and so do some relatives of clams, among other animals. One kind of Paramecium has symbiotic algae, etc. In these cases, the symbiotic plants can (usually? or always?) be cultured separately from the animal) A few kinds of animals have symbiotic bacteria in their cells. And we depend on symbiotic bacteria in our intestines. Mitochondria evolved from symbiotic bacteria. (it is even known which sub-group of bacteria!) Chloroplasts evolved from another symbiotic procaryote. There are theories that 2 or more other kinds of eucaryote organelles may also have evolved from symbiotic procaryotes. (But no one can prove if this is true or not, so far...) Mitochondria and chloroplasts have lost so many genes that they can't live separate from their "host cell"; but they are essentially degenerate procaryotes. But each chloroplast contains many copies of its genome, so it actually contains more DNA than a bacterial cell. Some geneticists study the genes of the DNA in chloroplasts, and that is what my wife's research is about. When she isn't posting web pages as a favor to me. In the eggs of frogs and some other animals, there are so many mitochondria that the majority of the DNA is mitochondrial! To almost everyone's surprise, it has fairly recently been discovered that some of what were thought to be bacteria are actually fundamentally different, and have some of the features of eucaryotes (histones, for example). These are classified as Archaea. (a third major subdivision) Some species in this group live in hot springs (even boiling!) Others live deep underground, or in other extreme environments Viruses are even more fundamentally different. & classified separate from procaryotes, eucaryotes or archaea Viruses are parasitic genetic material, that cannot live separately from whatever organism it is parasitizing. Some infect animals, others infect plants; others infect bacteria. (it isn't known if any infect chloroplasts, but it's conceivable!) Many viruses use DNA as their genetic material; other viruses use RNA, instead. Many human diseases are caused by viruses; some cancers are caused by certain viruses; and viruses have been VERY useful in cancer research, to reveal which genetic changes cause all kinds of cancers! Textbooks usually do not consider that viruses are alive. But that seems like a meaningless argument to me. The two main theories about the origin of viruses are a) They evolved from genes that "escaped", and went into business for themselves b) They evolved by extreme degeneration of parasites. Sometimes viruses that infect one kind of animal will become able to infect another kind of animal: "Emerging viruses". AIDS is caused by a virus that came from Chimpanzees and a certain kind of monkey. Parvo is another emerging virus, that got into dogs, and killed millions of them a few years ago. A dog disease (distemper) got into seals and even dolphins, and killed millions of them. SARS is another example; and if it or some equivalent animal disease gets loose among humans, it might kill 20 or 30% of the people in this room within one year. In 1918, three quarters of a million Americans were killed in one winter, by a special form of influenza that is still as incurable as it was then.   Possible exam questions: You should know the answers to all these questions, except the ones that have stars*. * One star means it's a specially difficult question, few of which would be asked on any one exam. ** Two stars means it's such a difficult question that I wouldn't really ask it, unless it was for extra credit. *** Three stars means: If you can figure out the answer, then please tell me, because I can't figure it out! 1) What are some examples of eucaryotic organisms? (can also be spelled eukaryotic) 2) What are some examples of procaryotic organisms? (can also be spelled prokaryotic) 3) Besides viruses, are there any organisms that are neither procaryotic nor eucaryotic? What are they called? 4) In what kinds of environments do members of this third group of organisms tend to live? 5) Which of the three groups of organisms have plasma membranes? (hint: all of them do.) 6) Where is the plasma membrane located? 7) Compare the location of the genes (DNA) in procaryotes versus in eucaryotes. 8) Which organisms use their plasma membranes for (among other purposes) chemiosmotic conversion of chemical energy from one form to another? 9) Are you more closely related to sea weed or to bacteria? (evolutionarily; and in terms of the structure of your cells) 10) Are the mitochondria in your cells more closely related to sea weed, or to bacteria, etc.? 11) What did chloroplasts evolve from? 12) What are 4 examples of organelles? 13) Do any organelles have their own genes (coded for by DNA located inside themselves, rather than in their cell's nucleus). 14) *Do their DNA contain ALL the genes needed to make them? 15) Is it possible to do genetics on the genes located in mitochondria and/or chloroplasts? 16) *Can you figure out some of the effects produced by mutations in the genes of mitochondria, or the effects of mutations in the genes of chloroplasts? 17) *Mitochondria and chloroplasts cannot continue to grow and reproduce outside their cells; but can you guess whether cells can ever continue to live if they lost all their chloroplasts, and/or mitochondria. 18) If so, then what wouldn't those cells be able to do, anymore. 19) *There is a rare species of amoeba that doesn't have any mitochondria, but does have symbiotic bacteria in its cytoplasm. What function do you suppose that these mitochondria serve? 20) What are some examples of animals that have commensal algae in their cytoplasm? 21) **Suppose that a one-celled animal had symbiotic (meaning the same thing as "commensal") algae in its cytoplasm (eucaryotic algae, I mean!), then if the animal cytoplasm and nucleus gradually became reduced in size during evolution, then would scientists mistake it for a kind of alga, itself; and would they think that the commensal alga cells were just chloroplasts? (Euglena were recently discovered to be examples of this!) 22) **What kinds of evidence might you look for that what seems to be a plant is really an animal with symbiotic algae nearly filling all its cytoplasm? Hint: count membrane layers in the "chloroplasts"? Look for locations of DNA? Compare DNA bases sequences with various animals? 23) The endoplasmic reticulum is an example of a what? 24) How many layers of membrane are there around a nucleus? 25) *Do you solemnly promise never to call plasma membranes "cell walls", or the reverse? 26) *How is it possible that in frog eggs, the great majority of the total DNA is in mitochondria? Hint, they have millions of mitochondria, but only one nucleus? 27) **About what year would you guess that the complete DNA base sequence of human mitochondrial DNA was determined? Hint: you may not have been born yet. 29) What are two alternative kinds of theories about the evolutionary origin of viruses? 30) Viruses use what as their genetic material? Hint: and what else? in some kinds of viruses. 31) ***Are there any viruses that infect chloroplasts, or that infect mitochondria? 33) *** Are there any kinds of viruses that infect species of archaea? (Let me know if you find out; I can't think of any reason why there wouldn't be; but I never heard of any examples) 34) If an animal is infected with a viral disease, are you likely to be able to catch that virus (become infected with it, and thereby made sick)? 35) If, somehow, you DID become infected with a virus that had previously only infected some kind of animal, then would your symptoms probably be worse, or not as bad, as the animal's symptoms? 36) What is an example of an animal disease that recently made such a "jump" to infecting humans? 37) **Guess some possible dangers of transplanting organs from animals into people. **What about potential dangers of using animal tissue culture cells and animal embryos to make vaccines against human diseases. 38) **Why do you suppose that eucaryote cells don't use their own plasma membranes for chemiosmotic energy coupling? (In terms of evolution? Because of ion concentrations in their environment? Because they let somebody else do it for them?) 39) *Many species of viruses infect and kill bacteria, but cannot infect eucaryotic cells: so suggest how such bacterial viruses might be used to treat human diseases that are caused by bacteria. 40) **Cancer results from failures of some mechanisms that restrain growth and DNA synthesis in the cells of our bodies: And the body defends itself from many kinds of virus by the self-destruction of cells in which viruses are detected. Based on this knowledge, how could viruses be engineered to cure cancer?

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