September 14: Procaryotes, Eucaryotes, and Organelles


Bacteria are procaryotes
Blue-Green algae (cyanobacteria) are also procaryotes

(one of several kinds of photosynthetic bacteria, that used to be classified with the algae)

The differences between procaryotes and eucaryotes are much more important than the differences between you and an amoeba, or you and a pine tree, or kelp, or mushrooms, etc.
(all of which are eucaryotes, as are humans and all other animals.

Procaryotes don't have nuclei; they have circular DNA chromosomes just floating in their cytoplasm.

Procaryotes don't have other organelles, either (mostly)
No nuclei, no mitochondria, no endoplasmic reticulum.

Also no histone proteins, no microtubules, no mitotic spindles.

Bacterial "flagella" (by which they swim) turned out to be completely different from eucaryote flagella.
They only look alike; but work completely differently.
They rotate like propellers, rather than wiggle like fish.

Only about 5,000 species of procaryotes have been "described"!
(formally studied and given a Linnean name, like E. coli etc.)
But almost certainly there are millions of different species.

Archaea are a recently-discovered taxonomic group, somewhat more complex that procaryotes, but almost like bacteria.
But they are different enough NOT to be procaryotes;
nor are they eucaryotes (& not quite missing links, either)

Archaea DO have histone proteins, for example.
So it's a fundamentally different group.
Some of them live at very high temperatures, almost boiling.
Others live in very high salt concentrations, etc.
and other extremes.

All other living things, animals, plants, fungi, protozoa, etc.
(including all algae except for the Blue-Greens)
are classified as Eucaryotes

Eucaryotes have their genes on multiple linear chromosomes
inside a nucleus, surrounded by two nuclear membranes
(the inner nuclear membrane and the outer nuclear membrane)
the textbooks prefers to call them "Nuclear Envelopes" for some dumb reason.

Nuclei have nuclear pores. These control stuff going in & out
{The structure of nuclear pores was discovered primarily by Prof. Joe Gall, who taught me cell biology in the spring semester of 1966, and taught me "Optical Methods" in the spring of 1968, and is a wonderful scientist, & never mentioned what he discovered}

The DNA of eucaryotes is tightly bound to special kinds of protein called histones (which are extremely conservative in evolution, with almost exactly the same amino acid sequence in humans as in, say, peas; only 2 different, out of hundreds)

Another organelle that (almost) all eucaryotic cells have are mitochondria. These also have inner and outer membranes.
They are special biochemical factories for energy generation.
They have their own DNA and genes; and evolved from symbiotic bacteria! (billions of years ago)

Plant cells have chloroplasts, which are yet another organelle.
Chloroplasts have THREE layers of membrane!
They make sugar using light energy ; "Photosynthesis"
They also have their own DNA and genes; and evolved from symbiotic blue-green algae!!!

Another organelle is the Endoplasmic Reticulum
It consists of sacks of membrane in the cytoplasm of many but not all kinds of cells, animals, plants, fungi, etc.
(only one layer of membrane, for a change!)
It is used for making proteins for export from the cell.
(smooth ER as compared with rough ER)

One of the major researchers on the ER was George Palade,
originally from Romania, who worked at the Rockefeller Univ.
and then at Yale Med. School. I may tell a joke about him.

There are other organelles, including vacuoles, lysosomes, and something called the Golgi Apparatus.

Each kind of organelle has its own special kinds of proteins.
The mechanism that puts these proteins into the correct organelle uses special parts of the proteins (often the N-terminal 15 or 60 amino acids) as an address. "signal peptide"

"Put me in the nucleus" is: Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val
"Keep me in the ER" is -Lys-Asp-Glu-Leu-Carboxy end
"Put in peroxysomes" is ----Ser-Lys-Leu----
"Put in mitochondria" is alternating + charged and hydrophobic
(memorize the concept, NOT these sequences!!)

Special proteins already in each kind of organelle membrane grab any copy of "their" signal peptide, and pull it and all the rest of whatever protein it is attached to, and pull it into that organelle.

This was proven by experiments in which genes were changed so that certain proteins began with the 10 or 20 amino acid sequence that some other protein would normally have; which caused these altered proteins to get put in the wrong organelle.

"Motor proteins" several kind of cytoplasmic proteins in eucaryotes can exert mechanical forces by sliding along fibers.
These are in eucaryotes, and NOT in procaryotes!

Myosin protein slides actively along fibers of the protein actin
Dynein and kinesin slide actively along microtubules, which are made of the protein tubulin.

Actin and myosin were first discovered in muscle cells, the active contraction of which is caused by sliding of large myosin fibers relative to actin fibers.
But almost all other kinds of cells have their own actin and myosin; many different kinds of myosins, in fact.
Amoeboid locomotion is also caused by these proteins; not only in the (several different) kinds of protozoa called amoebae,
but also in nearly all the cells of our body, which use this locomotion for wound healing, embryonic development, and movements of white blood cells. Cancer results from loss of control of this cell locomotion, as well as loss of growth control.

Dynein sliding relative to microtubules is what causes the bending of cilia and flagella; and also transports membranes and other materials from place to place in the cytoplasm.
Kinesin transports other materials around the cytoplasm.

Actin and microtubules form a meshwork called the "cytoskeleton" in most eucaryote cells, including nearly all human cells.
Each microtubule, and also each fiber of actin, has a "plus end" where more tubulin (or actin) tends to be added,
and a "minus end" from which tubulin (or actin, in the case of actin fibers) is more likely to be lost back into solution in the cytoplasm. In this case, the words plus and minus have nothing to do with electrical charge, or anything like that.
UNC and Duke have been among the world centers for studies of cytoskeletal proteins (especially this department)

Questions that you should now be able to answer:

1) Which of the following are eucaryotes?
People? Trees? Mushrooms? Kelp? Bacteria? Blue-green algae? Other kind of algae? Protozoa? Archaea?

2) What structures do eucaryotes have that procaryotes don't?

*3) Which have flagella? Procaryotes or eucaryotes?

4) Where is DNA located? In procaryotes? In eucaryotes?
(where else? in eucaryotic cells?)

5) Who has circular chromosomes?

*6) About how many different species of bacteria are known to science? About how many species of animals? Which probably actually has more species? Are any still to be discovered?

7) What did mitochondria and chloroplasts evolve from?
What is some of the evidence for this?

8) What are some other organelles?

9) What are nuclear pores, and how many layers of membrane are there in nuclei?

10) By what sort of mechanism are mitochondrial proteins, nuclear proteins, or other organelle proteins caused to become located in these organelles?

11) What kind of mutation could cause one of them to get put into the wrong organelle, or to go to none of the organelles?

12) What are histones; where are they located; and which kinds of organisms have them? And which don't have them?

13) Why are tubulin and actin not considered to be motor proteins, although they are the two most important cytoskeletal proteins.

*14) If microtubules usually polymerize outward from a center near the nucleus, then would you expect to find their plus or minus ends near the edges of the cell?

*15) Can you figure out what is meant by saying that a dynein is a minus end-directed motor protein, while all myosins and (almost all!) kinesins are plus end-directed?

*16) If membranes of the endoplasmic reticulum tend to contain kinesins, while membranes of the Golgi apparatus attach to dyneins, then how can that explain the positioning of these organelles in living human cells?

**17) Can you guess whether cancer cells usually exert stronger or weaker pulling forces, as compared with equivalent normal cells, as they undergo amoeboid locomotion? What about forces exerted during amoeboid locomotion of white blood cells, as compared with structural cells (i.e. stronger or weaker?) Would you expect cancer cells' amoeboid locomotion to be more like that of white blood cells, or more like that of cells in wound healing?

**18) Certain poisons specifically prevent tubulin from forming microtubules; would you expect that these poisons would be useful in treating any particular human diseases?

*19) Can you invent some alternative possible reasons why treating cells with these tubulin poisons will cause the cells to contract more strongly than before? (about 2 1/2 times as strong)
(a fact discovered in this department in the late 1980s)

*20) These poisons prevent normal separation of the chromosomes when plant and animal cells divide: can you invent two alternative kinds of possible mechanism, one involving kinesin, and the other nicknamed the "Pac-Man Hypothesis"?

***21) Can you figure out why histone proteins and actin have changed less than any other proteins in evolution, in the sense of having almost exactly the same amino acid sequences in humans as in plants, etc. (If you can think of reasons, please tell me)

22) Nerve fibers can be as long as 2 feet (distance from nucleus to most distant parts of the cell); How would you guess that new proteins get transported to such distant locations?

23*) Based on your suggested answer to the previous question, why would you expect that all the microtubules in the longest nerve fibers would have the same orientation (+ versus - ends), even though shorter nerve fibers contain about equal numbers of microtubules oriented in both directions (= as many with one polarity as the opposite)?

24*) Several kinds of bacteria that cause food poisoning turn out to use the actin of the infected cells to move around! Guess how they do this!

25**) Just before eucaryotic cells divide, their chromosomes gravitate to positions half way between the ends of the cells: how can this be made to happen by making strengths of pulling forces toward the ends vary as functions of each chromosome's current position in the cytoplasm




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