All proteins start with methionine at their N-terminal end;
and there are also sometimes methionines in the middle, etc.
One of the uses of methionine is to transfer methyl groups.
1) There are two different kinds of asexual reproduction:
A) by budding, as in Hydra, sponges, sea squirts, flatworms, etc.
(and also in many, many plants)
B) by development of non-fertilized egg cells
(as often happens in aphids, and many other animals)
2) The advantage of sexual reproduction (mixing genes from 2 parents) is a seriously difficult puzzle of biology (much debated)
Notice the "2-fold advantage" (twice as many embryos per parent)
if there were only females in a species.
Some species of fish and lizards have only females, also flatworms
this gives a short-range reproductive advantage, but for some reason
such species apparently get weeded out before long (but how?)
since > 1% of species abandon sexual reproduction
(although tens of thousands of species use both sexual and asexual rep.)
Another question is: even if you are going to recombine genes. etc.
why do so many animals have separate male and female sexes
(in contrast to higher plants, in which this is the exception)
3) "gametes" are eggs and sperm
" germ cells" are eggs and sperm,
and the precursor cells that develop into egg cells and sperm cells
"gonads" are the ovaries and the testes
(the anatomical organs where the egg cells and sperm develop)
4) In animals, for some unknown reason, the germ cells (almost?) always develop from a special kind of migratory cell that crawls actively from some other part of the body to the gonads.
These are called "primordial germ cells"
in many species, special particles or other special cytoplasm in the egg cell controls which embryonic cells will become the primordial germ cells.
{QUESTION: what if you graft primordial germ cells from one embryo to a genetically different embryo?}
5) Some species have big, yolky egg cells, with lots of stored food
Other species have relatively small egg cells
(only ~1000 times the volume of average somatic cells)
But even in the latter, "oogenesis" requires hyper-activity of the chromosomes, = very high rates of transcription.
all 4 sets of chromosomes are retained until the "last minute"
meiosis (reduction divisions) do not occur until the end of oogenesis.
and the cytokinesis is very unequal: produces 2 or 3 polar bodies
In most species (including humans) the second meiotic division doesn't occur until AFTER FERTILIZATION!!
(so the egg cell is triploid for a short while after fertilization!)
In some species (flies are an example), 15 mitotic sister cells fuse their cytoplasms into the oocyte (egg cell), as a way of storing more food
these fusing cells are called "nurse cells"; but no vertebrate does this!
6) In contrast, sperm cells develop after meiosis.
P.G.C. meiosis-> 4 haploid cells --> each one becomes a sperm
7) "Polyspermy" will result in a triploid embryo, which will either abort spontaneously, or in some species can become a sterile individual
(>20% of human pregnancies abort spontaneously, for various reasons)
So special mechanisms have evolved to prevent any more sperm from getting to the oocyte, once the first one has fertilized it.
these mechanisms are called "blocks to polyspermy"
Fertilization causes depolarization of the oocyte resting potential
& oocytes have voltage-gated sodium channels;
so they propagate the equivalent of an action potential across their plasma membrane; and calcium channels also open; so there is a wave of increased calcium concentration.
Among other results is release (exocytosis) of 10,000 +
cortical granules : secretion of their contents
Many (lower) species have an electrical fast block to polyspermy:
because depolarized membranes won't fuse! (could one say that they "refuse" to fuse?)
Several kinds of slow blocks to polyspermy result from secretion of the contents of the cortical vesicles:
* formation of a "fertilization membrane" (as in sea urchin eggs)
* enzymes specifically digest the proteins by which sperm stick to eggs
This digestion of adhesion molecules is what happens in mammals
(and is known as "the zona reaction")
Embryonic development in a nutshell
I) Cleavage (a series of 6-12 or fairly-rapid mitotic divisions)
(except in mammals, these divisions are quite slow)
many kinds of animals (frogs, flies, etc.) "turn off" the cell cycle checkpoints for these earliest divisions [but mammals, including humans, are an exception to this rule]
The result of these cleavage divisions is a ball of cells:
in many species (urchins, frogs, humans) a hollow ball of cells.
this is called the blastula stage of development
II) Gastrulation, and other morphogenetic cell movements
Cells of the blastula stage actively rearrange, by means of cytoplasmic acto-myosin, gains and losses of various cadherins, and other mechanisms yet to be discovered
Many or the cells that had been on the surface move actively into the interior.
III) the 3 primary germ layers:
Each differentiated cell type expresses a certain subset of genes
"housekeeping" genes are expressed in all cell types
"luxury" genes are expressed only in certain differentiated cells
Thus, differentiation consists of the expression of a specific subset of the total number of genes. (transcription of those genes)
"Determination" consists of commitment to express those luxury genes
Embryonic cells always become determined before they differentiate.
V) Determination occurs before (visible) differentiation.
The textbook prefers to say the cells have a memory, including a memory of what hasn't happened yet!
Sometimes cells can lose their (visible) differentiation, but still remain committed to the same cell type, if they do redifferentiate.
VI) The transcription factors that control determination and differentiation are often homologous, even in insects vs. humans!
This really was a big surprise: everyone assumes/d, for example,
that legs, eyes, segmentation, etc. had evolved completely separately in insects as compared with vertebrates.
Nevertheless, the amino acid sequences of the transcription factors
used to "turn on" the genes specific for a leg, or eye, etc. are often
much too similar not to have a common evolutionary origin!!
An especially interesting example of such homology is "hox genes".
These were discovered in flies, because mutating them can cause
legs to develop where antennae should develop,
and other "homeotic" changes.
Such mutations in flies all turned out to be changes in a family of genes
that were A) linked in two groups and B) had almost the same amino acid sequence in the part of the protein that binds to DNA
"the homeodomain" (coded for by the DNA homeobox)
The position of these genes along the chromosomes were correlated with the location in the body 1) where m-RNA was transcribed
and 2) where abnormalities occurred when the gene was mutated
This correlation between chromosome position and anatomical expression is also found in vertebrate hox genes.
"Colinearity" is a major unsolved problem!!
--> in plants, the equivalent of homeotic mutants produce substitutions of leaves in place of flower petals, etc.
VII) In some kinds of animals (nematodes & flies) embryonic development is exactly the same each time (sterotyped=mosaic)
Nematodes are an extreme example: each C elegans has 959 cells etc.
Cell lineage is exactly the same in one worm as another.
But mammals are at the other extreme (very "regulative")
identical twinning; embryonic fusion --> chimeras
(few seem to know: but some wasps are even more regulative!!)
VIII) Two kinds of mechanisms can be used to control cell fate:
1) Special molecules segregated into cells at or before cleavage
2) Signal molecules that pass from cell to cell ("induction")
IX) Mutations in flies have led to the discovery of many specific proteins used for both these kinds of signalling.
Very often, m-RNA for a given protein will be concentrated in some particular part of the embryo, & the protein will be made only there.
(patterns seen by "in situ hybridization" and also by antibodies)
Mutations produce anatomical abnormalities in these same parts!
X) The "wiring" pattern of the nervous system is produced by guidance of locomotion of nerve growth cones
many map-like connection patterns form ("neural projections") such as the connection between the retina of the eye and a part of the brain called the optic tectum. "retino-tectal connections"
Experiments show selective adhesion (and repulsion) in gradients: and maybe simultaneous action potentials influence competition "those that fire together, wire together"
Notice that we are skipping chapters 22 & 25
(although they are both interesting)
Please don't forget that the eventual goal of cancer research is to discover methods for selectively killing cancer cells. researchers seem to forget this
Any consistent abnormality of cancer cells might be a target.
So what somebody should do is invent a poison that will kill only cells that have the abnormality!
I) Cancer IS body cells that have lost their normal control of cell division (the cell cycle) and also their control of locomotion.
But cancer cells DON'T really grow faster than normal cells.
(but most anti-cancer drugs were designed on this assumption!)
If they just lost control of growth, then a benign tumor results.
If they also lose control of cell locomotion, then growing cells can also spread actively from place to place -> malignancy
metastasis : analogy to spread of primordial germ cells
Statistics indicate that 1/4 of the US population will get some fatal form of cancer (if you count skin cancers, 50%)
& 1/5th of us will actually die of cancer (at present cure rates)
(note that about 1/5th of the 1/4th will actually be cured by chemotherapy and/or surgery)
However: sometimes major cures get discovered
Until about 1950, tuberculosis killed more Americans than cancer.
Then streptomycin and another drug were discovered!
and nearly all cases became fully curable; this could happen with cancer.
II) Cancer cells (almost?) always retain many or most of the properties of the differentiated cells from which they arose.
carcinoma = cancers of epithelial cells
sarcomas = cancers of mesenchymal cells
leukemias and lymphomas are cancers of white blood cells.
there are even cancers of primordial germ cells, etc.
Cell types that can't divide don't form cancers (nerves, etc.)
III) Although cancer can be caused by certain virus infections
(many animal examples: such as cat leukemia, chicken sarcomas)
Maybe ~ 6% of human cancers caused by (venereal) papilloviruses
(related to the viruses that cause warts)
in humans great majority are due to somatic mutations in certain genes,
(although discovery of these genes owed a lot to studies of viruses)
cancer-critical genes oncogenes
often the over-activity of many of these genes: myc, bcl-2
or certain over-active protein: ras, src
sometimes underactivity of other genes: Rb
IV) Oncogenes ("cancer-critical genes") all code for proteins that are important, normal and necessary parts of signaling mechanisms that control normal cell behavior.
Sometimes newspaper or magazine articles suggest that if we could just get rid off all the oncogenes, we would be O.K.
That's removing the steering wheels, brakes etc. from cars!
Your cells couldn't live without the oncogenes, but somatic mutation of these genes changes them in ways that allows growth and movement to go out of control.
V) Probably most or all cases of actual cancer result from 3 or 4, or 6 different oncogenes becoming mutated in the same cell.
What's the evidence for this?
1) Statistical rates of cancer increase exponentially with age!
2) "Tumor progression" = getting worse & worse, etc.
3) Often, you can actually find mutations & chromosome breaks
4) Abnormalities in one oncogene destabilize the cell's mechanisms for preventing further mutations, etc. p53 etc.
VI) The causes of cancer in humans are nearly all mutagens
If a chemical can cause mutations, then it can almost always cause cancer; and vice versa...
but with some interesting exceptions
The cancer-causing chemicals in smoke (incl. tobacco smoke)
are converted into mutagens (DNA-reacting chemicals) by enzymes in the body that are meant to detoxify poisons.
Therefore, the standard test for carcinogenic chemicals uses rates of bacterial mutation, after the chemical has been treated with enzyme extracts from mammal liver cells.
Aflatoxin is a cancer-causing chemical produced by fungi in peanuts; like the chemicals in smoke: not a mutagen until detoxified
Another interesting exception is that frame-shift mutagens tend
not to be very strong carcinogens: do you see why that makes sense
VII) Nearly all anti-cancer chemotherapy drugs have been based on poisoning fast growing cells:
damaging DNA (nitrogen mustards, base analogs, antibiotics
tubulin-binding poisons vinblastine, taxol
But since cancer cells don't really grow faster than normal cells
it has been a paradox why any of these drugs ever cure anyone!
One solution to this paradox is stated as a fact in paragraph 3 on page 1356 of our textbook;
the idea is that normal cells protect themselves from the chemotheraputic drugs by halting the cell cycle until the damage is fixed
VIII) A few drugs are now being designed to block particular enzymes that are abnormal in certain kinds of cancer. "Gleevec" the Philadelphia chromosome, and all that...
IX) But cancer cells have dozens of reasonably consistent abnormalities, almost none of which are ever thought of as possible targets for new anti-cancer medicines.
X) Maybe YOU can invent some new and better treatments!
I won't test you on this history, but it may help you to understand some of the difficult facts about immunology.
First some basic facts:
1) The body attacks germs with a certain kind of protein called antibodies.
Each antibody molecule has 2 (or 4, or 10, depending on which kind)
binding sites, which have just the right complementary shape to bind to some molecule on the germ.
The molecules to which these binding sites bind are called antigens. (& "epitopes")
This name comes partly from the fact that secretion of a given antibody can be stimulated by injection of molecules of that antigen.
(the name also reflects one of the mistaken theories)
An antibody that binds to molecules of a given antigen is said to be an antibody "against" that antigen.
FOR EXAMPLE, antibodies against the type A blood group antigen would exactly fit the shape of the sugar chains on the cell surfaces of people (like me) who have type A blood.
These sugars are the antigen.
The antibody binding sites bind selectively to these sugars.
(but if I made such antibodies, I would be allergic to myself!)
2) As in other proteins, the shape of the binding site is caused by the amino acid sequence of the antibody protein in that part of the protein. Thus, for example, if you denature molecules of antibodies against a certain antigen, then when you let these protein molecules renature, they would re-form
the same shape binding sites as they had before.
3) (Vertebrate) animals can make antibodies against billions of different antigens! Ideally, they can make antibodies that will bind to every possible shape of molecule, EXCEPT not to the shapes of any of the molecules of their own body.
Please stop and notice how strange this is! Antibodies against different antigens each have different amino acid sequences at their binding sites! But we can make thousands of times more different antibodies that we have genes!
4) The DNA that codes for the binding sites of antibodies are constructed by splicing together random selections of certain base sequences.
This is analogous to drawing cards from a deck of cards.
For example, if you randomly drew one club, one heart, one spade, and one diamond, then how many different alternative combinations would there be?
13 x 13 x 13 x 13 = 28,561
(Ace. 2, 3...Jack, King, Queen is 13 cards)
Thus, if you constructed the DNA coding for the base sequences of the binding sites of antibodies by splicing one sequence from each of 4 sets of alternatives, then you could make binding sites with 28,000 different amino acid sequences
and therefore 28,000 different shaped binding sites.
Actually, this random splicing chooses one from each of 5 sets
and some of the sets have as many as 100 alternatives.
so there are millions of alternative combinations
Each binding site is made by a combination of a heavy chain (big protein) and a light chain (small protein)
genes for the light chains are spliced from 2 sets of alternatives
genes for the heavy chains are spliced from 3 sets. 2 + 3 = 5
VERY IMPORTANT: this splicing is done randomly in each lymphocyte (of the kind that eventually makes antibodies)
During your own embryonic development, billions of lymphocytes do this splicing, each lymphocyte thereby constructing a gene for making antibodies that have some particular (random, but consistent!) shaped binding site.
The point is to make all possible combinations;
then you keep some of the results, & throw away others.
This is called the clonal selection hypothesis.
Inventing this idea was one of the greatest achievements of mental creativity that any human beings have ever done, both in terms of difficulty and mental importance.
Niels Jerne, Macfarland Burnet & Joshua Lederberg did it.
what they did ranks with Mozart, Michelangelo or Archimedes
The idea came 30 years before the actual genes were found;
and no one could have known where to look, without the idea.
And chemically-oriented scientists were the main opponents of these ideas, but then took credit for them when they turned out to be correct.
One of the interesting aspects of this mechanism is the analogy to Darwinian evolution of species. Lymphocytes evolve during each person's lifetime, in somewhat the same way as species evolve over millions of years. It was where Jerne got the idea!
5) The cells that make and secrete antibodies are called B-lymphocytes
Another kind of lymphocyte called T-lymphocytes makes another kind of protein, that has analogous binding sites, the genes for which are also made by splicing a different set of alternative DNA sequences, and that are also used to fight germs; but these proteins stay stuck to the surface.
T is for thymus "cellular immunity"
B is for bursa of Fabricius "humoral immunity"
"immunoglobulin" is a synonym for antibody
Each B-cell makes antibodies all of which have exactly the same shape binding site; because they all have exactly the same amino acid sequence in their binding sites.
And when a B-cell divides, both daughter cells continue to make antibodies with this same exact shaped binding sites! (that's what it was called the clonal selection hypothesis)
The same is true of the amino acid sequences and the shapes of the binding sites of each given T cell: they are all identical with each other, for any given lymphocyte.
but different from one lymphocyte to another.
6) Molecular biologists eventually tracked down the actual DNA base sequences that get spliced, and also the enzymes.
V is for Variable sequence regions
D is for Diversity (in heavy chain genes, but not light chains)
J is for Joining region
C is for constant sequence (codes for the rest of the antibody)
(and there are several alternative constant sequences, just to make things even more confusing)
The splicing process that makes the genes for the variable sequence regions of antibody genes is called V(D)J recombination.
The enzymes that cause this process are called RAG proteins
Additional diversity (differences in base sequences in the genes for the binding sites) results from at least 2 other processes
A) They don't always splice at the same base pairs.
B) Very high rates of random mutation. "affinity maturation"
7) Because this system is random, it generates lymphocytes that make antibodies against everything, including yourself.
Books frequently say that the immune system "recognizes" antigens as being foreign. That vocabulary is a fossil of the old, pre-clonal selection theories about how immunity works.
Actually, foreign molecules need not have any common features.
If your immune system attacks germ: we call that immunity
When this system attacks pollen, poison ivy, etc.= allergy
And this system is equally capable of attacking normal molecules of the body: autoimmune diseases
T-cells attacking myelin sheaths = Multiple Sclerosis
Antibodies against DNA, membranes, etc. = Lupus
& dozens or hundreds of other autoimmune diseases
Antibodies attacking other antibodies! rheumatoid arthritis
8) The least-understood part of the immune system is the part that selectively weeds out just those B and T lymphocytes whose binding sites fit any of the body's own molecules.
This is called the tolerance mechanism.
When the tolerance mechanism works, your immune system only attacks foreign molecules. When even a little bit goes wrong with the tolerance mechanism, then you get an autoimmune disease. You could cure those diseases if you figure out how the anti-self lymphocytes are eliminated
9) In principle, the tolerance mechanism could work in any of the following ways:
A) Kill those B or T cells whose antibody or receptor binding sites bind to any self molecule.
B) Inactivate any anti-self B or T cell (make it so it can't make antibodies, or can't move, or gets trapped somewhere, etc.
C) "Re-program" anti-self lymphocytes, in the sense that they would repeat the V(D)J recombination, so as to make binding sites with different amino acid sequences.
D) Some kind of competition between lymphocytes, with a relative disadvantage to those that make anti-self binding sites.
There is some evidence for each of these types of mechanism. Grafting or injection of foreign cells into early embryos results in induced tolerance.
10) Vaccines work by stimulating multiplication of those lymphocytes whose binding sites fit molecules of a certain germ. Vaccines are one of several forms of antigens.
Some vaccines consist of killed viruses; other vaccines consist of molecules isolated from germs; some are modified forms of enzymes or other toxins made by germs; others are live, but weakened viruses or bacteria.
11) Histocompatibility antigens are certain kinds of cell surface proteins (on cells except red blood cells) that the immune system attacks especially strongly.
The reason for this strong attack is that histocompatibility antigens are key parts of the immune system's methods for cell-cell signalling.
For example, one kind of histocompatibility antigen holds up peptide fragments from that cell's cytoplasm, as a means of signalling if that cell is infected by some virus. If virus peptides are detected in the binding sites, then T cells kill initiate that cell's apoptosis.
12) Some new inventive concept may be needed to cure and prevent autoimmune diseases. And while you are at it, please invent a way to cause one of the many abnormalities of cancer cells to set off their own apoptosis. For example, invent an artificial peptide, small enough to leak into cells, but that only cancer cells would cleave into fragments that would fit into histocompatibility antigen binding sites.
You students now have the facts and concepts you need to do great things, as long as you don't believe that everything is already known. There is lots of neat stuff still to be done!
So don't sell your book! Re-read it for fun after the exam.