Olympic B3 Science Summer Camp 2014
Biotechnology, Biodiversity and Bioinformatics
June 11th - June 26th
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Vocabulary
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An idiosyncratic list of words used in class, further defined. Definitions are intended to make class discussions clear and may not be strictly accurate or complete. Requests are welcome!
- Pathogen: disease-producer. An agent of disease, something that causes the disease, usually an infectious microorganism, which includes bacteria, viruses and some fungi and oomycetes.Hosts with immune systems
will figure out how to recognize and then kill the pathogen. Vaccines are a shortcut that allows the process to occur without a high level of infection occurring first. Antibiotics and fungicides are small chemicals that kill the micro
organism but not its host. Organisms that do not have immune systems, like plants, often naturally make small chemicals that function as antibiotics. They also kill off parts of themselves that are infected so that they are isolated or fall away from the main part of the plant.
- Host: an organism that harbors a parasite, or a symbiotic organism, giving it shelter and nourishment. A pathogen is one kind of microbial parasite, the others are protozoans and fungi. There are also larger parasites, like worms and insects,
that may live inside an organism but not inside its cells. Some microorganisms that have a host are not considered parasites because they contribute to the welfare of the host (perhaps by providing vitamins that the host does not make itself), and do not take more than they give (peaceful co-existance).
- Ubiquitous: seeming to be everywhere at the same time.
- Monadnock: an isolated hill of rock that sticks up from a surrounding plain. Usually this happens because it is made of harder rock than the surrounding area (for example, volcanic versus limestone), so it does not erode as fast. Pilot Mountain and Crowder's Mountain in North Carolina are both examples of Monadnocks.
- Kyanite: is a mineral. The name in Greek refers to deep blue, the color of the crystals. It forms where Silica and Aluminum are present and have been under strong pressure
- Accuracy:This tells you how close a measurement is to its true value. You can have lots of measurements that are close to the true value but are not close to each other (accurate but not precise) . To verify accuracy of a device you usually need to refer to a basic physical property like mass, or to something calibrated to such a standard.
- Precision:When you make measurements multiple times, the precision is how often you get the same value. You can have lots of measurements that are close to each other but none of them are close to the right value (precise but not accurate) - that is, you get the same wrong answer over and over: good precision but lousy accuracy.
- ReproducibilityWhen talking about a measurement, this means the precision. When talking about an experiment this means that the predictions are the same (individual measurements might not show the same precision, but the overall effect is to give the same result).
- Sensitivity:For a measurement device this means the smallest change in the thing measured that gives you a detectable response - if the change is too small for the device then the change will be invisible to it (and you). Measurement devices usually have markings that indicate the resolution that the manufacturer has calibrated for (for some beakers we used it was +/- 50ml, for graduated cylinders it was +/- 1 ml and for
our micropipetters it was +/- 0.5 microliters. You should check that the apparent calibration marks really mean something, though.
- Measurement: Figuring out how much of some property a sample has, for example mass, volume, temperature or time. Measurements use scales, in some units like ounces or liters or seconds. Scientific measurements use agreed upon, standardized scales, like the metric scale so that when we report a quantity using a calibrated device someone else using a similarly calibrated device will get the same value for that quantity.
- Buffer: A water-based solution that has a chemical additive that compensates for changes in acidity by altering its state to keep the original acidity. In biology these are used to protect biological components in the solution from being altered, harmed or destroyed. Tris is one of the most commonly used biological buffers.
- Dissolve:In chemistry one chemical is dissolved in another when every atom of the chemical is interacting with and surrounded by atoms of the liquid, and it stays that way. There are related concepts of solvation, solubility, liquifaction, complex formation and dissolution, so this is a lot more complicated than my definition can handle.
- Precipitate:The formation of a solid (something not dissolved) in a solution during a chemical reaction, with the result that the part that is not dissolved will settle out (if it is more dense than the solution part).
- Centrifuge:a piece of equipment that spins a sample at high speed so that it experiences a high relative gravitational force - this speeds up gravity if you are waiting for something to settle out of a solution. You can do lots of other things with this too!
- Polymer - a molecule that is a long chain of repeating smaller units, usually of a relatively small number of types (3 or 4 to 30 or 40) and usually of one main chemical type (amino acids, or sugars for example). They can be natural, like proteins, or man-made, like plastics. The order of the subunits
affects the specific properties of the polymer
- Polysaccharide - polymers whose simple subunits are carbohydrates (sugars). They can be linear or branched, and include starches as well as plant cell wall components.
- Deoxyribonucleic acid (DNA) - a natural polymer whose subunits are the four nucleotides Adenosine, Guanosine, Thymidine and Cytosine. This polymer forms the genetic material of inheritance and instructures, that carries the information coding for how living cells develop and respond to their environment.
- Electrophoresis - the motion of charged particles through a solution when there is an electric field acting on the space. The particles will migrate at a velocity that depends on their charge and shape, and any barriers that they must move around.
- Homogeneous - a substance that is the same everywhere, no matter how big or small the volume examined
- Cuvette - this is a small tube (round or square) with a standard width, sealed at one end to hold solution and tranparent to particular wavelengths of light, so only the sample will absorb or emit light when placed in a spectrophotometer.
- Spectrophotometer - an instrument use to study how molecules interact with light, whether transmitting it, absorbing it, or emitting light at a new wavelength under some conditions. Usually you measure intensity of light at some wavelength before and after it passes through a sample that occupies a particular volume.
- Biotechnology - the use of living organisms or processes that first occurred in living organisms to make commercial products.
- Bio-engineering - applying tools of physics, math and chemistry to design and manufacture living organisms. The goal is to change how they interact with their environments. Because living systems are so complicated, this often requires biochemistry, molecular biology, mathematics, chemistry and physics as well as computer science tools.
- Bio-informatics - using computers to organize and manage data in order to apply tools from mathematics (like statistics) and computer science (like pattern discovery) to uncover new relationships.
- Genomics - refers to a particular type of experimental genetics that seeks to identify the sequence of all the DNA and RNA in organisms and then to understand the functional parts (genes, for example) and how they interact to make the phenotype of the organism
- Phenotype - is the label for all of the observable, measureable characteristics of an organism, from the visible to the molecular. It includes behaviors and procsses as well as physical structures.
- Genotype - is the inherited genetic instructions that an organism carries in its nucleic acids, that limit the number of ways the phenotype can be expressed.Every individual is slightly different, either because the DNA is different or because the interaction with the environment has made the way the instructions have been carried out slightly different.
- ELSI (Ethical, Legal, Social Implications and Issues arising from the Human Genome Project) - Sequencing the human genome (s) means that information that might be considered private or that might lead to bias against an individual (in job or insurance applications, for example) might occur in ways that we have not protected against.
This is an NIH funded effort to foresee and consider the ethical problems that might arise and provide well-considered policy suggestions to lawmakers and other decision-making bodies.
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