Sunday, August 24, 2014

Mutualism, parasitism, and commensalism

Mutualism: 

This is a beneficial relationship to both partners of different species living together. For example a bee and a pollinating flower. The bee gains nectar from the flower for survival, as it uses the bee to carry its pollen to other flowers. So both organisms living together benefit from their existence.
Parasitism: 
Parasites are completely dependent on a host for survival. The relationship is beneficial to one, and harmful to the other.  Parasites may live outside or inside a host; they are called ectoparasites (the prefix ecto means outside) and endoparasites (the prefix endo means inside). An example of the endoparasite is the tapeworms which live in the digestive systems of its host. Examples of ectoparasites are ticks and lice.
Commensalism: 
The association of two or more partners living together, where only one benefits from the partnership and the other remains unharmed.  An example of this is the relationship between a sea anemone with and a clown fish. The anemone travels with the fish on route to its destination and the fish remains unharmed.

Function and monomers

Monomer: Monomers are single units that make up the polymer (which are proteins, lipids, carbohydrates, nucleic acids). 


  • The monomer of proteins are AMINO ACIDS. A bunch of amino acids make up proteins. That is all a monomer is, a building block for a larger unit. 
  • The monomer for lipids are hydrocarbons. 
  • Monomers for carbohydrates such as starch and glycogen (polysaccharides) are single sugar units called monosaccharides. Monosaccharides are sugars such as glucose and fructose, polysaccharides are larger sugar molecules such as starch and glycogen. 
  • Monomers for nucleic acids, such as DNA and RNA, are nucleotides. 

Functional group: Groups of atoms within a molecule that interacts n predictable ways with other molecules. 
  • Functional groups for carbohydrates are hydroxides, and short hydrocarbons such as methyls and ethyls.
  • Functional groups for nucleic acids are small sugar units, nitrogen bases, and phosphate groups.
  • Functional groups for lipids are hydrocarbons, esters, carboxyls, hydroxol, and hydrocarbons. 
  • Functional groups for proteins are amines, ammonias, carboxyls and 20 remainder groups, which you probably wont need to know. 


Organic compounds



  1. Protein: come in a variety of structures and serve many functions. Protein is the major component of a cell's dry mass (i.e. next to water, cells are mostly protein). Some proteins serve a structural function (e.g. cytoskeleton), control chemical reactions (enzymes), provide motion (e.g. cilia, flagella), facilitate intracellular transport (e.g. motor proteins), and may play a role in intercellular communication (e.g. hormones, gap junctions, ligand-receptor binding, ion channels, etc.). Proteins are produced by ribosomes from mRNA templates, either in the cytosol or at the surface of the RER (for cytosolic or secreted proteins, respectively). 
  2. Fat: (dehydrated carbs) is major part of the cell membrane, also provides energy storage and insulation in animals. Lipids are produced in the SER.
  3. Nucleic acid: DNA stores our genetic information (cookbook for proteins, etc.); DNA is found in the nucleus of eukaryotes, hence the name nucleic acids. DNA is by far the largest molecule in a cell. RNA comes in a few varieties, including mRNA and tRNA which are involved in protein production. mRNA and tRNA are found in the cytosol, not the nucleus. 
  4. Carbohydrate: (sugars) provide readily available energy. While ATP is the energy carrier in the cell, in animals, glucose carries energy between cells by way of the blood. In plants, starch is the main energy-storing carb, not glucose. 


Dissolved oxygen lab

link to lab bench

Purpose: 

  1. To be able to measure the amount of dissolved oxygen in water samples at different temperatures
  2. To be able to analyze the effect of varying amounts of light on primary productivity
  3. To fully understand what the ideal light conditions are for O2 to be dissolved in H2O

Procedures: 
1.The aquatic sample must be rich in photosynthetic organisms — water that is so algae-rich it appears green is good for this activity.
2.Keep the water samples in a very bright light during the 24-hour period. Fluorescent bulbs do not give off much heat, but if you use an incandescent light bulb, you will need to place a heat sink (such as a beaker filled with water) between the light bulb and your bottles.

Typical results: 

Lab bench questions:




Lab bench quiz: See in paper copy (could not attach on blog as it was saved as a PDF)



Evolution evidence

  • Ancient Organism Remains: Darwin found many types of remains of ancient organisms. In addition to fossil layers, he saw other fossils, bones, insects in amber (hardened tree sap), and petrified wood. Another type of preserved organism, which Darwin did not find, is animals such as mammoths frozen and preserved in ice.
  • Fossil Layers: Sedimentary rock forms in layers, with the oldest at the bottom and the youngest at the top. Fossils in the bottom layers are very different from the organisms alive today; Darwin didn't even recognize them. As one looks farther up, at younger and younger rock layers, the fossilized plants and animals become more and more familiar until they are a lot like organisms that are around now. The organisms also tend to become more and more complex. From this, Darwin concluded that organisms have not remained the same since earth's beginning, and that they have changed a lot, gradually becoming more and more complex. He also realized that as new species arise, other ones become extinct.

  • Similarities Among Living Organisms: One type of evidence for evolution (evidence that organisms are related, descended from a few common ancestors, and change to adapt to their environments) is that organisms are similar to each other, but not exactly the same. Similar organisms have differences that help them adapt to their environments. Many organisms have similar body plans. Horses', donkeys', and zebras' bodies are set up in pretty much the same way, because they are descended from a common ancestor. As organisms adapt and evolve, not everything about them changes. The differences, such as the zebra's stripes, show that each species adapted to its own environment after branching off from the common ancestor.
  • Similarities of Embryos: The study of one type of evidence of evolution is called embryology, the study of embryos. An embryo is an unborn (or unhatched) animal or human young in its earliest phases. Embryos of many different kinds of animals: mammals, birds, reptiles, fish, etc. look very similar and it is often difficult to tell them apart. Many traits of one type of animal appear in the embryo of another type of animal. For example, fish embryos and human embryos both have gill slits. In fish they develop into gills, but in humans they disappear before birth.This shows that the animals are similar and that they develop similarly, implying that they are related, have common ancestors and that they started out the same, gradually evolving different traits, but that the basic plan for a creature's beginning remains the same.

Natural selection

Natural selection is the gradual process by which biological traits become either more or less common in a population as a function of the effect of inherited traits on the differential reproductive success of organisms interacting with their environment. It is a key mechanism of evolution. The term "natural selection" was popularized by Charles Darwin who intended it to be compared with artificial selection, now more commonly referred to as selective breeding.

Examples:

1. Humans

Are humans still evolving? The simple answer is yes, even if the changes are not obvious. Experts believe that about 9 percent of our genes are undergoing rapid evolution as we speak. The genes most affected by natural selection are those involving the immune system, sexual reproduction and sensory perception.
Lactose intolerance is one example of natural selection. We are the only species that doesn't become lactose intolerant as we grow up. According to experts, this seemed to have happened when cattle became domesticated in Europe centuries ago. Another example is the sickle hemoglobin gene, which occurs in people who live in certain regions of Africa and other areas where malaria is endemic. This gene mutation makes people who have it more resistant to malaria. While they can still contract the disease, they are less likely to die from it. The mutation probably happened over hundreds of generations as a result of the constant exposure to malaria and people contracting and surviving it

2. Lizards

A number of studies have been done on lizards to determine natural selection. One experiment temporarily eliminated the lizards' natural predators from a particular area, and then scientists observed what impact that had on the lizards. The surprising find was that it's not so much the predators that influence the death or survival of certain lizards. Instead, the smaller lizards were more likely to die off anyway despite the lack of natural predators, because the larger, stronger lizards in the area still had better access to food. The lizards with the longest legs were able to climb better, escape the ground when floods or storms came, and reach food that wasn't available down below.

3. Nylon-eating Bacteria

Since nylon wasn't invented until the 1940s, bacteria that can eat nylon can be nothing but new. The bacterium Pseudomonas is able to metabolize nylon thanks to certain enzymes it has. However, a surprising thing happens when you take a non-nylon eating variety of this bacterium and place it in an environment where the only type of food available is nylon. Every single time the experiment was tried, the bacteria would evolve until it was able to consume nylon. This is a very simple example of natural selection, where the most basic forms of life can adapt to whatever food the environment offers.

  • Regressive Evolution: the disappearance of traits that were once useful but now obsolete. One example is the existence of eyes on Mexican cavefish, a species found in subterranean caves. Because of the caves' perpetual darkness, eyes became no longer necessary and eventually fish were born without them. Cave-dwelling fish have also lost their pigmentation and have become nearly transparent, since they no longer need camouflage because of the lack of natural predators

4. Deer Mouse

Nebraska's Sand Hills is home to a deer mouse that's one of the quickest-evolving examples of natural selection in animals. The deer mouse is normally dark brown, which is a good color for mice living in the woods and surrounding areas, since it allows them to hide better and avoid predators. The deer mouse that lives in the Sand Hills, however, has evolved into a much lighter, sand-like color. Without this change, the deer mouse would be easily spotted by predators against the area's light terrain. Just one single gene had to change for the mouse's coat to become lighter. What's even more impressive? The change took only about 8,000 years, which is the equivalent to seconds in the evolutionary scale 

5. Warrior Ants

The warrior ants in Africa are probably one of the most impressive examples of adaptation. Within any single colony, ants emit a chemical signal that lets the others know they all belong to the same compound. Or, put more simply, a signal that says "Don't attack me, we're all family." However, warrior ants have learned how to imitate the signal from a different colony. So if a group of warrior ants attacks a colony, they will be able to imitate that colony's signal. As a result, the workers in the colony will continue on, now under the direction of new masters, without ever realizing an invasion has taken place.

6. Peacocks

The more impressive the tail of a male peacock, the higher its chances of finding a mate. Female peacocks choose mates based on the color of the feathers and the overall physical prowess of the animal. According to experts, the brightness of the plumage might signal to females that the animal has high-quality genes. This would make him ideal for reproduction and to ensure the survival of the offspring, so they're chosen first when it's time to mate. In reality, not all males have bright, large tails, and this was especially true a few thousand years ago. And because females kept choosing the brightest males as partners, the ones without the impressive tails were less likely to mate and reproduce. As a result, their numbers diminished from one generation to the next, making them rare today.

Darwin v. Lamarck

 Jean Baptiste de LamarckCharles Darwin
Conception of species:
Population of individuals all of the same kind (identical characteristics in all members). Individuals capable of transformation.
Population of interbreeding individuals with similar characteristics, though variation is common among all of them at all times. Individuals fixed and unchanging. Population capable of transformation.
Mechanism of new species production:
Internal drive toward greater complexity modified by the inheritance of acquired characteristics. Change directed to meet organism needs.
Natural selection. Variation exists regardless of organism's needs not directed toward any purpose.
Example of this type of explanation:
The giraffe's neck: “At some point in the past, giraffes must have found themselves in an environment where they had difficulty reaching food present on the tops of trees. In order to eat, they must have had to stretch their necks and in doing so physically elongated them some. This longer neck was passed on to the offspring in the next generation, who in turn stretched their necks even further, thus resulting in the giraffe species having very long necks."
Keen eyesight of the hawk: “In a  population of hawks, individual  variation existed in the power of  their vision, just as variation exists  in the color of their feathers. In  their competition for food, the  individuals with keener eyesight  could more easily spot their prey  (small voles and mice) and thus  were successful in securing food to  eat. The hawks with poor eyesight  had difficulty spotting prey and  died for lack of food. The hawks  with the keen eyesight passed on  this trait to their offspring. The  hawks that died were not able to  produce any offspring. Over a  number of generations, the  population of hawks all came to  possess extremely powerful vision."
Phenomena the model can account for:• Adaptation
• Fossil record
• Adaptation
• Fossil record
• Homologous structures
• Biogeographical diversity patterns