Older blogs below

Enzyme Screencast

Here is a link to a screencast from last year, I think, about enzymes and energy. It's 55 minutes long. But, you might find sections of it helpful. Kate: you might especially benefit from this. Read More...

Endocrine Review



Hormone: the signaling molecule
Gland (endocrine gland means "no ducts." Secrete around cells, distribute through the bloodstream)
Steroid hormone: kind of a special case. Does not have a receptor on the surface of the target cell. Carried through the blood bound to special carrier proteins and diffuses through the membrane of the target cell. The receptor is a transcription factor.
Neurosecretory cell. Just like any neuron except they are not in a synapse with a specific target cell. Instead, their neurotransmitter is released where it can get into the blood or target nearby cells.
Homeostasis: This is the central point of the endocrine system. Negative feedback loops keep things right about where they are. The system has evolved signals and counter signals that push back and forth against each other to keep things right about where they should be (or, at least, where they are).
There are only a couple of "positive" feedback loops that do not do this.

General Outline

Don't memorize lots of glands and hormones.
You should assume you will see some feedback loop I have not presented before and be asked to answer questions about it…such as "what would happen if…?"
Also, review the neuro stuff as well.

The key points are:
The brain is the central controller for the endocrine system. The main units are the hypothalamus, which secretes many important hormones and the pituitary, connected to the Hypothalamus. It stores and secretes hormones from the hypothalamus as well as making its own. The other gland is the pineal gland, also in the brain, which mainly controls sleep (makes the hormone melatonin).
Many of the hormones of the hypothalamus and pituitary are "tropic hormones," which target other endocrine glands. They have names like "Thyroid Stimulating Hormone" (guess what that does).
Hormones work in context:
Same hormone can result in different effects in different cells (may have different receptors or different signaling pathways or both)
Same hormone can have different effects based on presence or absence of other signals (other hormones, for example).


There are few distinctions between nervous system signaling except for the distance and speed of action (possible exception of steroids, as mentioned above). Many of the same mechanisms are involved and the two directly interact with each other. In fact, neurons can directly impinge on endocrine glands to cause them to release hormones. Many hormones are similar to or even identical to neurotransmitters. The mechanism of release is the same as we have seen before.

Hormones are released to have an effect on target cells throughout the body. Target cells have receptors for the hormones.
Not all cells react to the same hormone the same way. This may be because the different cells have different receptors. It may be because they have different signaling pathways connected to the receptor.
None of this is surprising in light of what you already know. Each cell has a limited set of things it can do…let's call them programs or subroutines. The hormone epinephrine binds to a receptor and the target cell runs it's "epinephrine routine." That routine is different in different cells.
Hormone signals interact both directly and indirectly. Two hormones may exactly counteract each other's signal (like glucagon and insulin) achieving homeostasis by the "yin and yang" of their functions. Also, hormone signals may modulate each other more indirectly. The effect of hormone "A" and "B" together may not be the sum of their individual actions, but instead combine to a new overall effect.

Homeostasis: With one or two notable exceptions (oxytocin being the main one) everything in this system is evolved to keep the status quo. I will include a figure on the test that talks about a system I haven't shown you before. You will have to read and interpret the figure.
The typical negative feedback system is where there is a signal, target cells respond, send a signal back to the origin of the first signal saying "I heard you, got it under control," and diminishes the original signal.
The rare positive feedback works differently. The target organ sends the signal "I heard you, give me more!" and things move off in a dramatic direction.
It might be interesting to think about "bad" examples of this. Depression can have a rather unpleasant "positive" feedback (positive is in quotes because the effects are "negative" with respect to health). The behaviors associated with depression are also behaviors that exacerbate depression.

Physics being physics

Dynamics of self assembly

This is absolutely the first time I have ever felt the need to embed someone else's video in my blog. I run a demo early in the year showing how simple rules and movement can lead to spontaneous assembly of complex structure. My demos with magnets are good and Art Olson's "shaker virus" demo is great. But, this is absolutely AWESOME.

Immunology Review

Some guidelines for the immune quiz

Barriers such as skin and mucus, tears etc. form initial barrier

Innate Immunity:

Cell and biochemical defenses against pathogens. These have four main roles:
  1. First responders attack intruders (some specific for particular types of pathogens using recognition receptors).
  2. Cells release pro-inflammatory signal molecules that attract other immune cells to the area (both more innate immunity cells and adaptive cells)
  3. Present antigens for adaptive immunity to surveil
  4. Following adaptation of B-cells and antibody production, some components of innate immunity are targeted more specifically to pathogen by the antibodies

Cells (really just some of them) The figure shows how red blood cell and thrombocytes (for blood-clot formation) derive from the same progenitor cells as the immune system. You don't have to memorize the details. Know B cells T cells (both types) and Macrophages (antigen presenting cells) like in the game.
Macrophage (big mouth). Know this one. Gobble pathogens up, present antigens to adaptive cells in the MHC receptor and release pro-inflammatory signal molecules (other antigen presenting cells include dendritic cells).
Weird-shaped nucleus cells (OK, that's not the official name. They are called "polymorphonuclear cells," which essentially means the same thing). They, along with mast cells, are the main source of the pro-inflammatory signals. They all have slightly different jobs and include the basophil (likes basic stain); neutrophil (neutral pH stain) and Eosinophil (likes acid stain). You wouldn't need to know what each of these do. But, you could get a figure that has them in it.

Mast Cells are probably the worst offender, along with basophils and eosinophils. Probably good to know Mast cells. They are the underlying inducers of allergies and anaphylaxis. Secrete lots of pro-inflammatory signals. Extra information: Eosinophils in particular collect special antibodies made by certain B cells called IgE, which they then use to attack all the multicellular parasites you have, like worms and such. If you don't have worms, they are fond of attacking pollen grains, etc.

Natural-killer (NK) cells. You should know these. Come from the same line as the cells of the adaptive immune system. Activated by macrophage signals, identify infected cells in the body and kill them

Adaptive Immunity

You should know all of this unless noted.
T-cells (thymus) and B-cells (bone-marrow).
B cells are the ones that make antibodies (also known as B-cell receptor prior to class switching).
Both T and B cells undergo "somatic rearrangement" of their DNA to express one and only one T-cell receptor or B-cell receptor. The enzymes that carry out the splicing of the DNA are called "Rag-1" and "Rag-2." (Recombination Activation Gene 1 and 2). This is known as "V(D)J recombination and it generates a different antibody
for each B cell line you have. A very similar thing happens in the T-cells. During maturation of B cells, one V (variable) region, one D region (diversity) and one J region (junctional) are brought together and linked to the Constant region to make the heavy chain of the antibody. The light leaves out the "D" and the C region.
The "antigen-combining site" is at the amino (NH2) terminus of each chain. This is what allows the antibody to bind the antigen.

Cytotoxic T-cells (also called "CD8-positive T cells") identify infected cells and other targets based on specific recognition by their T-cell receptor and secrete chemicals to kill them. They make their receptor through a similar process as the B cell (somatic recombination).

Helper T Cells
These are critical for the full response (and also the target of HIV. They have a T-cell receptor as does the killer. But, they look for B cells that have been stimulated by the same antigen. If they find one, they initiate the highly active response in the B cell in which the receptor evolves into an even more specific antibody. Eventually, the highly activated B cells undergo "class switching," which just means they initiate an alternative RNA splice that gets rid of the membrane-bound creation of the antibody and start secreting it as part of the soluble or "Humoral" response.

The main use of the antibody is then to target components of the innate immunity more specifically toward the pathogen.

I think that's the important stuff. Remember, I sugar wcan show you figures of things I haven't discussed, necessarily. Also, go over the terminology on the online quiz.

Neurotoxin Assignment

Here is the link to the activity in google docs.