BIOLOGY.1.LAB.MANUAL.WD
Laboratory Manual for General Biology BI 101
(24th Edition – Fall 2019)
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AN INTRODUCTION TO
SCIENTIFIC DISCOVERY
Dr. Jay Pitocchelli
Biology Department, Saint Anselm College
TABLE OF CONTENTS
INTRODUCTION 3
Chapter 1 THE MICROSCOPE 7
Chapter 2 PLANTS AND ENERGY 15
Chapter 3 DIFFUSION AND OSMOSIS 19
Chapter 4 CELL DIVISION AND MITOSIS 30
Chapter 5 GENETIC ARCHITECTURE AND KARYOLOGY 34
Chapter 6 BIODIVERSITY 48
Chapter 7 BIOLOGICAL CHEMICALS, NUTRITION AND HEALTH 63
Chapter 8 SEMINARS 74
Chapter 9 GEL ELECTROPHORESIS AND PROTEINS 77
Chapter 10 THE SCIENTIFIC METHOD AND TOUCH THERAPY 84
ACKNOWLEDGEMENTS 92
APPENDIX - THE BALANCE 94
Appendix - DNA Fingerprinting Simulation 96
Appendix on Student Seminar Evaluations 98
Appendix on A Student’s Quick Guide to Hazardous Waste Disposal 102
Appendix on Transcription and Translation 104
INTRODUCTION
The Science Lab and Scientific Inquiry
The first solid package of information about the field of Biology a student is exposed to is the lecture text. Students are amazed at the quantity of information, the number of pages, figures, pictures, graphs, etc.... There are usually two types of questions that come to mind. The first questions are usually financial. How much does that monstrosity cost? After I buy this tome, will I be able to buy texts for my other courses? After accepting the fact that they must endure the financial pain of purchasing the text, students should ask a series of course content questions. Where did all that information come from? How did the author(s) accumulate all those facts and figures? Who did all this work? How did they do it? Where did they get all the money to do this? One answer is all that work was done in thousands of laboratories all over the world and at great cost in terms of money, time, effort and sacrifice. Some of the laboratories were just like the ones you have seen on TV or in the movies; sophisticated and expensive equipment, glassware with glowing chemical reactions, rats, mice or monkeys in cages awaiting some unknown fate, greenhouses with plants that could kill or save lives, ordering pizza, ordering Chinese food at 11:30PM for the lab, chemical wonders and chemical spills, microscopes of all shapes, sizes and costs. Some of the materials in the text also came from field research similar to what you've seen on the Public Broadcast and Discovery Channels; the great field expeditions up the Amazon or down the Nile, bartering with aboriginal tribes for the right to collect plants and animals on their native lands, collecting critical data during the middle of a civil war in a third world country, trying to fight seasickness while conducting fisheries research in the middle of gale force winds, avoiding painful insect bites or poisonous snakes, battling horrible weather conditions just to find out if the male Gannet is really on top when "they do it." This is what Biology is all about, the adventure and excitement of discovery and the path it took to get there.
Unfortunately the text only superficially covers laboratory Biology, presenting "JUST THE FACTS, MA'AM." It leaves out all the interesting details about how scientists work, the excitement of being on the cutting edge of a discipline, to go where no person has gone before, the hard work, sweat, toil, late nights, computer breakdowns and computer breakthroughs that make science fun and exciting. Due to constraints imposed by the publisher, authors can't include all these true-life situations into a text. So the students are left with a lot of facts, figures, drawings, pretty pictures of plants and insect genitalia without much of a clue as to how all this knowledge we call Biology is discovered.
Sorry, we can't help out with financing the cost of the book but we will be trying to show you where all that information came from, how it is obtained and how scientists conduct research in the laboratory to answer questions about natural phenomena. The laboratory portion of this course is designed to take you through the process of scientific inquiry that Biologists go through when they conduct research. In these laboratories you and your fellow students will assume the role of principal investigator and go through the same process that scientists go through in real life biological experimentation. In each of the labs you will use the Scientific Method to answer biological questions (Figure 1). It will be the common thread that ties all the labs together. But what is the Scientific Method? Although there is a great deal of debate over the answer to this question and how each scientist uses the Scientific Method in their respective fields there is some general consensus that will prove useful here. A few of the important steps are listed below.
1) Assemble all of the relevant literature and research on a topic of
interest. Read and become conversant on the topic. Talk to
your colleagues and discuss your ideas. Two heads are
better than one!!!
2) Begin to search for the cutting edge of the research topic. Ask
questions about unknown aspects of the phenomenon.
Remember, you always want to contribute new information,
you never want to reinvent the wheel.
3) Design a project to answer a question from 2. Assemble all the
resources (chemicals, equipment, materials, people, etc...).
Set up the necessary schedules and arrangements. Try and
take everything into consideration and include contingencies.
If something can go wrong, it probably will and often at the
most inopportune times.
4) Collect and analyze the data. Make sure the data collection will
provide answers to questions raised in 2.
5) Interpret the data. What do all those numbers mean? Does your
data answer the questions raised in 2.
The most important steps are 1 and 2. Anybody can provide the answers but it is the person who comes up with the questions who is really thinking. In order to ask the questions you have to know and assimilate all the biological knowledge that has been accumulated on your topic, then decide what will be interesting to investigate further. You define the cutting edge of your discipline and then go after it.
During the labs this semester you will employ the Scientific Method. In each lab you will follow four important steps, which are listed below.
• BRAINSTORMING - discussion of a biological phenomena and
brainstorming new ideas testing different aspects or predictions
that are relevant to these phenomena (see 1 and 2 above).
Scientists just don't come into the laboratory and do labs. They think, create, argue, debate, ask questions and devise solutions to those questions. One of the most challenging parts of being a Biologist is asking the right questions. It first involves assembling what is known about a particular biological phenomenon. If you know what is known, then you also know what is unknown and deserves further research. This important step gives a scientist direction for new investigations.
For most labs you will discuss scientific questions amongst yourselves and your lab instructor. You will begin with a classic bull session where you discuss a new theory, mull over the relevant facts and devise experiments, which will try to answer new questions.
• EXPERIMENTATION - actually performing the experiments that confirm
or deny different aspects of a theory or phenomenon (see 3 above).
You will have different equipment and chemicals at your disposal for each lab. Make use of it in your experiments so you can test your theories and predictions.
• DATA COLLECTION - collecting, analyzing data from the experiment(s) (see 4 above).
Data is useless unless you analyze it (you knew that because now you're a legitimate bio geek). Computers will be on hand in the Biology Department's computer lab so you can input your data and display it instantaneously to see if it fits your predictions.
• INTERPRETATION - where you interpret the results (see 5 above).
This is when you ask yourself what happened during the experiment (see 5 above). What do the results mean? What are their implications? Do they fit predictions based on relevant theories? Do they answer the questions raised at the beginning of the experiment?
Finally, you complete the experiment, enjoy your success once you have solved that problem and then come in the following week and work on something else new and exciting. Each week you will set out on a new mission to seek out and explain other interesting and novel biological phenomena.
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Figure 1. The Scientific Method and its connection to the labs in Biology 1.
How to Use This Manual
Read the appropriate chapter before every lab!! What did I just say? Read the appropriate chapter before every lab!! Preparation is critical for several reasons. You will know the important facts about biological phenomenon you are investigating that day. Knowledge of background material is essential to experimentation. This will help you during the brainstorming session, which requires not only knowing the pertinent facts about the lab but also using those facts to devise experiments. You will not only be prepared but the lab will be a safer place to work in when you know what you are doing.
This manual also guides you through the lab manual, directing you to the experiments we will be performing and avoiding ones we won't be doing. Each lab exercise in the Manual follows the structure below. The Introduction contains background information about the lab you will perform on a given day and its relevance to current issues in Biology. The Outline of the lab shows you where to go in the Lab Manual for information and exercises for all labs. BRAINSTORMING through INTERPRETATION are treated above.
Introduction
BRAINSTORMING
Outline of the lab
EXPERIMENTATION
DATA COLLECTION
INTERPRETATION
There will be several sections in this manual for you to formally write down your ideas, estimates, guesses, predictions, data and interpretations. Do it!!! Perhaps one of the best reasons for reading this manual is that some of the lab quiz will come directly from it.
Safety
The laboratory is a safe place to work as long as you keep it safe. In some of the labs you will be handling potentially harmful chemicals, hot plates, glassware and power units for gel electrophoresis. Handle these carefully and ask your instructor when you have questions about handling these items. The best way to avoid accidents is to maintain a clean workspace. Clean up after yourself in the laboratory at your lab bench and the lab in general. There will be a protocol for emergencies posted in each laboratory. Make yourself aware of these procedures. The lab should be a safe and a fun place to work.
THE MICROSCOPE
AND A
FORENSIC EXPERIMENT
Introduction
This lab will introduce you to light microscopes and how to use them. You will first go over the different parts of the compound light microscope and their functions. Then you will do the same for the stereomicroscope (also referred to as the dissecting scope). It is very important that you learn how to use the microscope in this lab for several reasons. The microscope is perhaps the most commonly used tool in Biology. Every Biologist uses it at one point in their career. Therefore, in order to understand Biology you should understand how to use one of its most fundamental tools. The second reason is that you will be using microscopes often during the semester for different labs and you will have to be proficient in its use to successfully complete those labs.
In Part I you will practice using the compound and stereomicroscope with some sample slides and materials. These microscopes have different applications. The stereomicroscope is used to examine materials too small for a magnifying glass but too large for fine detail. The compound microscope is used for small specimens such as details of tissues or cells. Examine and compare the magnification power of both microscope and develop a sense of when to use one versus the other (see Appendix-Microscopy and the web page in your lab syllabus for parts of the microscope). Each microscope uses light, which bounces off the object and illuminates the specimen in contrast to the electron microscope, which uses electrons that bounce off the specimen to produce an image.
In Part II of the lab you become involved in a simulated exercise in forensic science. In the forensic part of this lab you will solve a crime by examining evidence from the crime scene and comparing that to evidence found on the suspects. Materials taken from real crime scenes are often analyzed using the light microscope. These are compared with materials found on the suspect, in the suspect's house or vehicle, etc. There is no better way to learn how to use sophisticated equipment than "on the job training." That's exactly what you will encounter in this part of the lab, learning how to use the microscope by solving a crime.
Part I. Become familiar with the parts of the microscope. Identify and learn how to use the following parts of the compound light microscope.
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|Microscope Parts |Notes/function |
|Ocular |Magnification = |
|Nosepiece | |
|Objectives | |
|Stage | |
|Specimen clips | |
|Diaphragm | |
|Light source and on/off switch | |
|Arm | |
|Coarse focus | |
|Fine focus | |
Begin using the compound light microscope by examining a series of slides of inanimate materials.
1) The letter e
2) Threads
Continue by examining some examples of live organisms. Make a wet mount of each specimen by placing a drop of water on a slide. Then carefully place a coverslip over the drop of water taking care to avoid water bubbles under the coverslip.
1) Paramecium
2) Volvox
For this next exercise you will make wet mounts of plant and animal cells. You will also learning the traditional staining technique. First prepare a slide of onion cells and then stain the cells with IKI. Make a wet mount of each specimen by placing a drop of water on a slide. Carefully place a coverslip over the drop of water taking care to avoid water bubbles under the coverslip. Place a small piece of paper towel up to one edge of the coverslip while at the same time putting a few drops of IKI along the opposite edge of the coverslip. The paper towel will draw the dye across the specimen. IKI will stain a yellow nucleus in the onion cells. Next, make a swab of your cheek cells and smear the cells across a slide. Add a drop of water and a drop of Methylene blue. Place a coverslip on the preparation and look for the stained nuclei in your cheek cells.
In order to gain a size perspective on the microscope, slide a ruler under the objectives and measure the diameter of the field of view (Figure 1.1). How wide is the field of view (in mm) in your microscope for each of the objectives? If there are 25.4 mm (2.54 cm) per inch, how many inches wide is the field of view in the lowest objective? Fill in the on the next page.
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Figure 1.1 Measuring the field of view with a millimeter ruler.
Objective Diameter (mm) Diameter (inches)
Low
Note - some microscopes only have two objectives (Low and High)!
Study the parts of the dissecting microscope. Notice the similarities and differences between the dissecting versus the compound light microscopes. Examine various specimens under the dissecting microscope.
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1) desiccated flies
2) computer chips
3) post cards
4) photographs
5) E. coli culture
6) B. megaterium culture
7) Bread mold culture
8) Fern leaves with sori
Part II. Using microscopes to examine biological evidence is an important component of criminal investigation. How often do you hear of cases where forensic scientists are brought in to help solve complex crimes? What are these scientists doing? How will they help solve crimes? They are brought in to perform a very specialized part of the investigation. They are looking for clues that only specialists would be able to find and give expert testimony on. They are often asked to examine chemicals, blood, semen, hair, feathers, etc.... Later, they may be able to determine whether there is a match between samples taken from the crime scene and those taken from a suspect. This may provide important circumstantial evidence that the suspect was at the scene of the crime (alibi or no alibi!!!).
In this crime some thief stole a case of Coors Cutter and a case of O'Douls. You are not that worried about the loss of the beer because you'd never drink that lousy excuse for a good lager anyway. What's really got you rip roarin' mad is that someone invaded your privacy and you want them to pay hard time for it (90 days cleaning up the toxic waste facility). You have been called in as a forensic expert to help police catch this purloiner of bad ale.
BRAINSTORMING
The result of your brainstorming in this lab will be to devise a plan to solve the crime based on the forensic evidence available to you. Discuss the larger details as well as the smaller details you feel are important. Following the questions and train of thought below will help you develop a plan.
You should start this part of the lab by discussing a few simple questions. How would you go about solving this crime? How would you collect data or evidence? How would you analyze the evidence in such a way that pinpoints the correct suspect as the appropriate defendant for an indictment? Your answers to these questions will dictate how you proceed with the investigation.
The following information is very important to helping you solve this crime. You will have to examine these clues and determine their usefulness for identifying the correct suspect as the actual criminal (you don't want to send an innocent person to jail!!!). The robbery took place at your home which has a pheasant farm where your breed pheasants for the state's propagation program. Your nosy next-door neighbors are witnesses who saw a person with light hair leaving the scene of the crime carrying two medium-sized packages. Luckily they banged their heads on the doorway, leaving a few hair samples and blood for inspection. Some cloth samples were taken from the scene, which are believed to have come from the suspect's clothing. The purloiner of your beverages stepped on some plants in your garden or brushed up against some flowering trees or plants with pollen granules that could be useful forensic evidence. Some vegetable materials were removed from all of the suspects for analysis. The suspects stepped on some potatoes in your garden but avoided the onion patch (hint - there are essential differences between onion and potatoes that can be picked up with stains). Pollen samples were removed from each suspect's clothing for close inspection for comparison with the pine tree pollen.
Develop a plan for this investigation and write down some of the key steps in the space below.
BRAINSTORMING SCRATCH SPACE
Experimental Design
Predicted Outcomes
Outline of the lab
Part I Learning the Light Microscope
Learn the parts of the compound and stereo microscopes
Some simples trial slides
Letter "e," threads, photographs versus printed pages
Pond water
Part II
Forensic lab
EXPERIMENTATION
Part I. Learn the parts of the microscope and practice with the appropriate materials in the laboratory. Follow these simple rules:
1. Always start with low power.
2. Always start with the smallest light setting on the diaphragm.
3. Always begin with coarse focus and work your way up to fine focus.
Part II. Implement your plan to find the correct suspect. Set up your modus operandi for data collection and do the work. Assemble the necessary materials and analyze them. Each lab table will have a suspect tube and a crime scene tube for analysis. Keep good and accurate records (see below) for your expert testimony in court.
DATA COLLECTION
Use the table below to collect information on each of the subjects. Then compare the suspects' results with results taken from the crime scene. The data below should either be Match –Yes or No Match- No.
Sample Table
Vegetable Matter
Suspect Feathers Hair Cloth Pollen Soil (Potato or Onion)
Bugsy No No No No No No
The King No No No No No No
Scarface Yes Yes Yes Yes Yes Yes
Bonehead No No No No No No
O. G. No No No No No No
You would report the evidence supports a conviction for Scarface
Your Results for the Entire Lab
Vegetable Matter
Suspect Feathers Hair Cloth Pollen Soil (Potato or Onion)
Bugsy
The King
Scarface
Bonehead
O. G.
Crime Scene
INTERPRETATION
Who done it? What are the results of your work and what do they mean? Who is guilty? Who should pay the stiff penalty for pilfering the non-alcoholic brew? In the space below write a few short sentences summarizing your data and why you chose one suspect over the others.
PLANTS AND ENERGY
Introduction
Rainforests are being disturbed at an alarming rate all over the world. Trees are used for lumber and the cleared land is used for farming or grazing. Why are we so alarmed over this process? One of the reasons is that the oxygen supply for all living, breathing organisms comes from plants when they undergo photosynthesis. Oxygen is a byproduct of this complex chemical reaction. Continued destruction of the tropical and temperate rainforest ecosystems will deplete the source and production of oxygen. In order to fully appreciate this problem you must gain an understanding of the process of photosynthesis and the production of oxygen. By examining the process you will better understand some of the consequences of human encroachment and destruction of our biological resources.
Photosynthesis is a chemical reaction in the leaves of plants where CO2 molecules are converted into a chemical energy in the form of a simple sugar (glucose). The O2, which we breathe, is also released as a product of photosynthesis (Figure 2.1). During the process, H2O, which enters the plant through the underground roots, is split using energy from sunlight in the form of photons that the plant is able to harness. O2 is released from the H2O molecule. The products of the photosynthesis reaction are O2, H2O and C6H12O6. C6H12O6 is a simple sugar called glucose that is stored in the plant as an energy reserve. Most plants build complex sugars called starches using glucose as building blocks. These starches are often stored in underground organs called tubers. Organisms that are able to synthesize their own energy in this manner are called autotrophs. Animals feed on glucose from plants for energy to fuel chemical reactions in their bodies. Animals are called heterotrophs because they are unable to synthesize their own energy. They must obtain it by eating autotrophs.
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Figure 2.1. Unbalanced equation for photosynthesis: reactants are on the left, products are on the right.
In this lab you will investigate different aspects of the photosynthesis reaction. In Part I you will perform an experiment on how energy from the sun is trapped by plants. Your work will address the following questions:
1. How do plants acquire energy from sunlight for the photosynthesis
reaction?
2. Do they accomplish it as efficiently as possible?
In Part II you investigate how chemicals involved in photosynthesis enter and leave the plant by examining slides of leaves. Your work will address the following questions:
1. Where do the chemicals for photosynthesis enter the plant?
2. Where do the chemicals for photosynthesis leave the plant?
Finally in Part III, you will observe how glucose or chemical energy is stored in plants. Your work will address the following question:
1. Where is the chemical energy from photosynthesis stored in plants?
BRAINSTORMING
Part I. We know the chemicals involved in the reaction. We know the reactants and the products but where does energy come from? We know that it is somehow tied to sunlight but how? What is the process? What is light? What are the properties of sunlight that provide energy?
The answer lies in color. Understanding the mystery of light, color, reflection and absorbance are the keys to understanding how plants harness energy from the sun. Although we call it white light, it is actually composed of many different colors that are not visible to the naked eye. We can only see the colors of white light when we use a prism to bend the light's rays (what natural event displays all the colors of white light?). White light is actually composed of several colors ranging from red at one end of the spectrum to violet at the other end (see the web page in your lab syllabus). The colors you see, like red, green, blue, yellow, etc. are the colors that different objects reflect. For example if your sweater is green then the sweater reflects green light but absorbs all the other colors. Different colors also have different energy contents. Colors at the extreme ends of the spectrum tend to contain the most usable energy (reds and blues) while intermediate colors like green tend to yield the least amount of energy for photosynthesis. Red pigments like carotenes donate their energy to other pigments at the reaction center.
Which wavelengths do you think plants would try and absorb energy from? How would you test which wavelengths are used most effectively by plants? Why? What is the color of most plants? Does that mean that they don't have any other pigments? What kinds of color pigments would you expects plants to have? If plants have different pigments then: where are they, do these pigments probably differ in some aspect of their chemical makeup and behavior? How would you know? How could you take advantage of these differences in separating pigments? (Hint - if you had 5 long-distance runners and wanted to find out who was the fastest how would you do it?)
Part II. We know the chemicals involved but where do they come from? Chemicals come in different forms - gas, liquid and solid. What forms are the reactants and products in photosynthesis? How does this affect how they enter and leave the plant? What and where should we look in plants to answer these questions?
Part III. Starch made from glucose is a chemical fuel stored in plants. Well, where is it stored? Where in the plant would you begin to look for it? How would you look for it? What would you use to find sugars stored in plants?
BRAINSTORMING SCRATCH SPACE
Experimental Design
Predicted Outcomes for each Experiment
Outline of the lab
Part I Chromatography
Use prepared extracts.
Part II Observe plant slides
Elodea - chloroplasts and cyclic movement
Tradescantia - guard cells
Part III Energy Storage in Plants
potato preparation and stain
EXPERIMENTATION
Part I. Set up an apparatus using the materials on hand, which will illustrate the presence of different pigment molecules in plants.
Part II. While this reaction is occurring examine the cross-section of a plant and identify the structures and their functions: Tradescantia (guard cells for gas exchange), Elodea (chloroplasts).
Part III. Examine the storage products in the following structures.
1) Potato
2) Sweet Potato
3) Yam
4) Rudebaga
5) Apple
6) Pear
DATA COLLECTION
Part I. Did you find different pigments? How do you know? Measure the distances traveled by the different pigments (before you take measurements, determine how will you measure the distance moved by chemical, e.g. where do you measure from and to?). Why do you think that these measurements are important? Fill in the table below, which summarizes your results.
Part II. Make a drawing of the plant slides you made. Using arrows, show the movement of gases in and out of the plant. Turn in one copy of the below per group.
Color of Distance
Pigment Traveled
INTERPRETATION
Now that you have finished these experiments and observations, how did your work answer the questions addressed in the Introduction?
DIFFUSION AND OSMOSIS
Introduction
The normal day-to-day activities of the body involve billions of chemical reactions inside cells. But in order for these reactions to take place chemicals must move in and out of cells. How do chemicals enter or leave cells? Most chemicals move in and out of cells through the process of diffusion. Diffusion is a simple property whereby chemicals move from an area of high concentration to an area of low concentration. When a cell does not have to use energy to move chemicals across the membrane, diffusion is a passive form of transfer of chemicals from one side of the membrane to the other. O2 and CO2 exchange between blood and alveoli in the lungs occurs by diffusion. Most hormones enter cells from the blood through diffusion. These exchanges take place because of simple diffusion gradients located at strategic points throughout the body.
There are some interesting questions about different aspects of diffusion. Chemicals must get their energy from somewhere to move during diffusion. Chemicals also come in different forms such as gas, liquid and solids. Chemists and Biologists are interested in whether chemicals in each of these different forms obey the laws of diffusion. In Part I of the lab you will address the following question:
1. Where does the energy come from for movement of molecules in diffusion?
In Part II of this lab you will investigate whether chemicals in different states are able to diffuse into each other and the effects of molecular size on the rate of diffusion.
2. Do gases diffuse into other gases?
3. Do liquids diffuse into solids?
Another interesting aspect of diffusion is that some chemicals don't pass freely through certain cell membranes. Some chemicals are harmful to the cell's internal chemical machinery because they disrupt or pollute important chemical reactions in the cell. In Part III of the lab you will address the following questions:
1. Are some membranes selectively permeable (e.g. do they let some chemicals pass
while preventing others) or completely impermeable, not allowing any
chemicals to pass through?
2. If they are selectively permeable how do they accomplish this?
Finally in Part III, we are interested in the effects of changing the external environment on diffusion, especially temperature. It has been shown that increasing temperature increases the rate at which molecules travel while cooling the environment does the opposite. In this lab you will address the following questions:
1. How will warming the external environment affect diffusion?
2. How will cooling the external environment affect diffusion?
BRAINSTORMING
Part I. You should discuss several questions related to movement. Are molecules constantly moving? How can we determine whether molecules are moving or stationary? If they are moving, is there a pattern to their movement? Where do they get the energy for movement?
Part II. Besides movement of molecules we are also interested in diffusion of chemicals in different states? Do gases diffuse in liquids? Do liquids diffuse in solids? How could we test for diffusion of chemicals in different states (e.g., gas liquid, solid)?
Part IIIA. If you were given an artificial membrane with small pores that were all the same size, how could you set up an experiment that would demonstrate that membranes are semi-permeable? Look at Figure 3.1 for clues and see if you can find devise an experiment.
You will design experiments on diffusion across plasma membranes of living cells (e.g., Elodea plants). How would you go about this? If you know something about the concentration of water inside the cell where would you go from there?
Part IIIB. We are interested in altering the external environment and observing the effects (if any) on diffusion. How would altering temperature affect diffusion? How would altering the concentration of salts or water in the external environment affect diffusion? Make predictions about what will happen when you alter the external environment.
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Figure 3.1. Impermeable (A) and semipermeable (B) membranes. Note that the semipermeable membrane allows the small black molecules through
but not the larger striped molecules.
BRAINSTORMING SCRATCH SPACE
Experimental Design
Predicted Outcomes for each Experiment
Outline of the lab
Part I Brownian Movement (ink or charcoal)
Part II Diffusion of molecules in various states - gases, liquids and solids
Diffusion of liquid in a solid (agar, IKI and Methylene Blue)
Example of diffusion of gas in a gas (cheap perfume)
Part IIIA The Role of Membranes in Diffusion
Thistle Tube demo
liquid in a liquid - thistle tube demo
Osmosis
Elodea and osmotic stress experiment
Part IIIB Effects of Temperature on Diffusion Across Membranes
Dialysis tubing experiment, hot and cold-water baths
EXPERIMENTATION
Part I. In order to describe the movement of molecules you will have to observe their movements under the microscope. You can't see small molecules so we will use a suspended charcoal solution or India ink particles, representing large molecules.
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Part II. You will also observe diffusion of gas within a gas. In this experiment you measure in seconds, how long it takes perfume to travel in the atmosphere of the room in feet (__ ft/sec). How many miles per hour (mph) is the perfume traveling? What factors do you think could affect gases as they travel through the atmosphere?
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You will also observe the diffusion of a liquid in a solid. In this experiment you will bore two holes in agar on an agar plate. Put a drop of IKI into one of the holes and one drop of Methylene blue into the second hole. Let the liquids dissolve into the solid agar until the end of the lab period. Compare the distances traveled into the agar by each liquid. Note that the IKI is a smaller molecule than Methylene Blue.
Part IIIA. The third part of the lab will be setting up your experiments on cell membranes. In order to observe diffusion your instructor will set up a thistle tube apparatus.
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Subject living cells to different concentrations of water and examine the results of this on the turgor pressure inside the cell. One solution should be hypotonic (having a lower concentration of salts or solutes outside than inside the cell) and the other should be hypertonic (having a higher concentration of salts or solutes outside than inside the cell). For the plant cell you should compare a cell exposed to both pure water and salty water. When the concentrations of salts in two solutions are the same they are isotonic.
Part IIIB. Besides observing diffusion you will investigate the effects of temperature on the diffusion process. Set up some dialysis tubes in a hot water bath and a cold water bath at each table. Label your bags so you know which one belongs to each group. Before putting your bags into the experimental baths make sure that you weigh them (why???).
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DATA COLLECTION
Part II. Place the perfume in the back corner of the room and have two observers at the front of the room. Measure the distance between the observers and the perfume. Time how long it takes until the two observers smell the perfume: ft/sec. Convert this to mph.
Conversion Example
Observed data = 40'/60 sec, same as 0.667'/sec
1) Divide 0.667' by 5,280'. This tells you that 0.667' = .00013 miles/sec.
2) There are 3600 seconds/hour (60 min x 60 sec) so multiply 3600 by .00013 miles to find mph.
3) The perfume is traveling approximately 0.455 mph.
Your Data
ft/sec
mph
Use the XL spreadsheet that will perform these calculations.
Part III. Fill in the table below with the weights of your dialysis tubing bags. Make sure that you enter the data for both the hot and cold-water baths.
Hot Water Bath Cold Water Bath
Before After Before After
Your data on the effects of different salt concentration (hypertonic versus hypotonic) outside living cells are your drawings. They are the only recollections of your comparative work on animal and plant cells so make some accurate drawings in the space provided below. Make sure you label these drawings so you know what they are and are able to show somebody else. Include the observable parts of the cell, power of magnification and a title (specific type of cell).
Plant Cell in Hypotonic Solution Plant Cell in Hypertonic Solution
INTERPRETATION
Now that you have finished these experiments and observations, how did your work answer the questions addressed in the Introduction?
CELL DIVISION AND MITOSIS
Introduction
How do organisms grow from a single-celled zygote to an adult with several billion cells? How does a tree over 100' tall grow from a sapling emerging at ground level? How do salamanders regenerate lost limbs or tails? How does your body repair itself after being injured? The simple answer is duplication of cells through the process of mitosis. Mitosis results in precise duplication of parent cells resulting in daughter cells. Salamander cells duplicate themselves to make more salamander cells. Mitosis occurs in trees, humans, fish and millions of other species.
Exact duplication is critical since errors in duplication can be fatal. Cancer is an example of when errors occur in mitosis. Duplication runs rampant and out of control, producing many non-functional cells that result in tumors. Since cancer is one of the leading causes of death it would be important to understand mitosis and its role in production of cancerous cells. In this lab you will investigate and observe the complex process of cellular reproduction, which results in precise duplication of daughter cells based on the original blueprint of the parent cell. In Part I of this lab you will become familiar with the different stages of cell division by examining prepared slides of cell division. In Part II of this lab you will make your own preparations of cell mitosis in onion cells. You will use a commercially prepared whole mount slide as a reference for identifying the different stages in the live onion preparation.
BRAINSTORMING
Part I. You are interested in observing the different phases of mitosis in plant cells (Figure 4.1). The cell spends most of its time in Interphase, a non-dividing phase where it performs its daily functions and prepares itself for duplication. During cell division it goes through several phases. These phases are characterized by the different positions of chromosomes inside the dividing cell. They are easily distinguished under the light microscope. However, cells differ in their microanatomy. For example, both plant and animal cells have cell membranes but plants also have a cell wall external to the cell membrane. How would cell division differ in these two major groups of organisms? Discuss these issues and how you might recognize differences between plant and animal cell division.
Part II. Where would you begin to look for dividing cells in a plant? Does mitosis occur everywhere throughout the plant body? Since you can't normally see chromosomes how would you make them visible?
[pic]
Figure 4.1. The cell cycle and Mitosis.
Phase Prominent Activities
Interphase growth and DNA duplication
Pro appearance of chromosomes
Meta chromosome line up along equator
Ana centromeres break and chromatids splits apart
Telo formation of cell plate in plants, segregation of chromosomes
Cytokinesis split of cytoplasm and formation of two cells
Outline of the lab
Part I Prepared slides (whole mounts)
Identify interphase and the stages of the mitosis on onion root tip
Part II Make slide from squashed onion preparation
Identify interphase and the stages of the mitosis on onion root tip
EXPERIMENTATION
Part I. Examine the whole mount slide(s) of mitosis and find the different phases. You should do this first so that when you make your own preparation of the onion slide later you will know what to look for because you will have already seen the different phases.
Part II. In order to make your own preparation of mitosis in the onion root tip, you will learn a technique of staining cells undergoing different phases of mitosis. It will be up to you to find all the different stages. Follow the instructions on the handout.
Part III. One of the best ways to learn mitosis is to simulate each of the different stages with a model. In this case the model will be pipe cleaners representing homologous chromosomes and plastic rings will be the centromere that binds homologous chromosomes together. Perform the simulation with two different homologous chromosomes and go through interphase, prophase, metaphase, anaphase and telophase with the pipe cleaners and beads.
DATA COLLECTION
Identify cells in interphase as well as all the stages of mitosis: prophase, metaphase, anaphase, telophase and cytokinesis.
INTERPRETATION
Make drawings in the space below of each of the different phases of mitosis in plants. Label each drawing.
Interphase Anaphase
Prophase Telophase
Metaphase Cytokinesis
GENETIC ARCHITECTURE AND KARYOLOGY
Introduction
The field of Genetics is one of the most rapidly developing disciplines in Biology. Geneticists are currently trying to map the human genome, locate genes responsible for genetic disease (e.g., Huntington's, Parkinson's, etc.) and provide gene therapy for victims of genetic disease. Industry has also teamed up with geneticists to find disease resistant crops or develop strains of bacteria to fight oil spills. Genetics has not advanced without some controversy. Jurassic Park is an excellent fictional example of a genetic engineering disaster. Although we are nowhere near the technology needed to recreate dinosaurs, releasing genetically engineered organisms such as bacteria or viruses into the environment could be extremely dangerous if they are not carefully tested in the laboratory and monitored in the wild. The role of genetic engineering in human genetics has been fraught with controversy since the eugenics programs of the United States in the early 1900's to Hitler's heinous experimentation during World War II. Since you will be confronted with some of these issues in your graduate life, it will be important to develop an understanding of some of the basic principles of genetics.
The DNA located on your chromosomes contains the genetic blueprint for your body's design. It is like a library of information on how to build your body. Part of that information came from your father and part of it came from your mother. The exact relationship between the genotype and your outward appearance or phenotype is the subject of intensive investigation in the field genetics. Mendel discovered some fundamental laws of genetics while studying genotypes and phenotypes of peas back in the late 1800's. Some genotype - phenotype relationships, like the one's studied by Mendel are straightforward while others are much more complex.
Mendel studied external characters of pea plants such as seed color, seed texture, stem length, flower color, etc. He studied the inheritance patterns of these characters over several generations in controlled breeding experiments. These external characters are now referred to as the phenotype. He learned that most characters came in two different forms. Seeds were yellow or green. Their texture was smooth or wrinkled. The stems were long or short. Through an analysis of the inheritance patterns of these characters he concluded that there were unseen particles in the plants responsible for the expression of the phenotype. These particles are now referred to as genes and they are found within cells of organisms. The genotype is the combination of two alleles, which are alternative forms of each gene. There is an allele for smooth (S) and one for wrinkled (s). For instance, SS or Ss or ss are three different genotypes, each having two alleles. Mendel also found that there are specific relationships between alleles. When two different alleles are combined in some individuals one of the alleles usually masks the phenotype of the other allele. In the texture example, S is dominant over s and smooth seed phenotype may be caused by SS or Ss genotypes. S is the dominant allele while s is the recessive allele. Individuals with SS or ss are called homozygous dominant and homozygous recessive genotypes respectively. Individuals with two different alleles are called heterozygous.
Where are the alleles located and why are there two alleles? Alleles are located on chromosomes. The reason there are two alleles is that there are two versions of each chromosome (called homologous pairs) and each chromosome contains one allele. For example, there are 46 total chromosomes in humans but they are arranged into 23 homologous pairs. The most famous pair of homologous chromosomes is the sex chromosomes: XX (female in humans, males in birds), XY (males in humans, females in birds). In the pea example above, S is located on one chromosome and s is located on another chromosome (both chromosomes form the homologous pair). There are some genes that are located on the sex chromosomes. These are called sex-linked alleles. Some genetic disorders such as hemophilia (blood clotting disease) are caused by sex-linked alleles.
In this lab you will study the relationship between genotype and phenotype by building fictional organisms called "Rebops" based on genes selected randomly from a gene pool. The goal of the exercise is to understand how genes contain information on the body's architecture and how the relationship between genes influences expression in the phenotype. There will be three exercises in this lab: Part I - building Rebops based on genetic information you have chosen from chromosomes, Part II - finding the parents of your Rebop among other Rebops in the lab, Part III - since your Rebops are feeling "the urge" you will also be able to mate them with other Rebops and determine the offspring. In this lab you will address the following questions:
1. How does a dominance relationship work between two genes?
2. How are recessive alleles that may cause genetic disease
maintained in populations?
3. What are sex-linked alleles?
4. How are genes expressed?
In the Part IV of this lab you will study human chromosomes. The study of chromosomes is called Karyology. It involves isolating chromosomes in dividing cells, staining the chromosomes and counting the chromosome number. Humans have 23 pairs of homologous chromosomes or a total of 46. Studying human chromosomes has led to some interesting discoveries and insights into human genetic diseases. Some individuals with genetic disease inherit extra chromosomes (greater than 46) while others are lacking chromosomes (less than 46). Trisomy or Down's Syndrome is an example of individuals that have inherited an extra chromosome # 21. These individuals are usually retarded, may suffer from heart defects and other physiological abnormalities. Some individuals lack a sex chromosome and are born X_. These individuals are sterile and fail to develop secondary sexual characteristics. In this exercise you will be given a set of chromosomes and you will match up the homologous pairs. You will then make a decision on whether the individual is normal or has a chromosome disorder.
You will be using a web site from the University of Utah where you will be given chromosomes and asked to match up homologous pairs.
[pic]
After you have matched the pairs, you will know whether you have an individual that is normal or has one of the genetic aberrations mentioned above. Your lab instructor will bring you up to the Weiler computer center to perform this exercise.
BRAINSTORMING
Part I. Building organisms from genes is much like constructing buildings from blueprints. How do constructions workers build a building? What role does the architect play? What is the role of the blueprint? How are genes and blueprints analogous? How would you build your Rebop based on the genes you have selected? Do you think there will be any twins? What do you think the chances of getting twins are? What sex is your Rebop? How will you know?
Part II. How would you go about finding the parents of your Rebop? What characteristics would they have? What kinds of genes would they have?
Part III. What kind of offspring would you expect if you mated your Rebop with a nearby male or female? How could you predict what your Rebop's offspring would be like?
Part IV. How will you be able to tell whether individuals have a normal genetic makeup or may be suffering from a genetic disease? Are you able to tell which diseases individuals might have based on their chromosome number?
BRAINSTORMING SCRATCH SPACE
Experimental Design
Outline of the lab
Part I Building Rebops
Part II Finding your Rebop's parents
Part III Mating Rebops
Part IV Karyology
EXPERIMENTATION
Part I. For each of the Rebop characters there are two alleles. Choose two alleles per character from each of seven envelopes. Each envelope contains alleles for different aspects of the phenotype. There is a dominant/recessive relationship between any two alleles for a given phenotypic character. Use the table below to determine which genes you have and how they will be expressed in the phenotype.
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Build the Rebop based on the genes chosen and their corresponding phenotypes. Record the genotypes and phenotypes for your Rebop, its parents, and the offspring of a mating between your Rebop and a nearby member of the opposite sex. Use Table 5.1 to find the appropriate body parts that match your selection of genes. Figure 5.1 shows a completed Rebop and the body parts.
Table 5.1. Genotypes and phenotypes of Rebops.
Genotype Phenotype
AA, Aa _________ tail (pipe cleaners)
aa _________ tail
QQ, Qq curly tail (pipe cleaners)
qq straight tail
EE _________ eyes (thumb tacks)
Ee one _________ eye, one _________ eye
ee _____ eyes
DD, Dd _________ legs (push pins)
dd _________ legs
MM, Mm _________ mouth (thumb tacks)
mm _________ mouth
TT, Tt _________ ears (short pins)
tt _________ ears
XLXL, XLXl, XLY _________ antennae (long pins)
Xl Xl, XlY _________ antennae (sex-linked genetic disorder)
XX female (without hump)
XY male (with hump - geometric shaped pins)
[pic]
Figure 5.1. Rebop and body parts.
DATA COLLECTION
Fill in the Table below. Build the parents and one baby based on the information below. Arrange the Rebops in each generation and show your lab instructor for verification.
Generation 1 – Parents of your Rebop
Generation 2 – Your Rebop and its mate
[pic]
Generation 3 – Your Rebop’s offspring
Your Your Possible Possible
Phenotypic Rebop's Rebop's Mother's Father's Mate's Mate's Baby's
Character Genotype Phenotype Phenotype Phenotype Genotype Phenotype Genotype/Phenotype
Tail color
Tail shape
Eyes
Legs
Mouth
Ears
Antennae
Sex
Workspace for determining parents
Example – Tail color, A – Green tails (AA, Aa), a – brown tails (aa)
Your Rebop Aa
|Gametes |a |a |
|A |AA |Aa |
|a |Aa |aa |
|Parents Genotype |Aa, Aa | |
| | | |
|Parents Phenotype |Green, Green | |
Tail color
Your Rebop ____
|Gametes | | |
|Gametes | | |
| | | |
| | | |
|Parents Genotype | | |
| | | |
|Parents Phenotype | | |
Tail Shape
Your Rebop ____
|Gametes | | |
|Gametes | | |
| | | |
| | | |
|Parents Genotype | | |
| | | |
|Parents Phenotype | | |
Eyes
Your Rebop ____
|Gametes | | |
|Gametes | | |
| | | |
| | | |
|Parents Genotype | | |
| | | |
|Parents Phenotype | | |
Legs
Your Rebop ____
|Gametes | | |
|Gametes | | |
| | | |
| | | |
|Parents Genotype | | |
| | | |
|Parents Phenotype | | |
Ears
Your Rebop ____
|Gametes | | |
|Gametes | | |
| | | |
| | | |
|Parents Genotype | | |
| | | |
|Parents Phenotype | | |
Antennae
Your Rebop ____
|Gametes | | |
|Gametes | | |
| | | |
| | | |
|Parents Genotype | | |
| | | |
|Parents Phenotype | | |
Part IV. This exercise will be performed on a computer using a web page with chromosomes from the University of Washington. You will be given a slide of chromosomes and you will have to match the homologous chromosomes using the mouse to move them together. Each partner of the homologous pair should look almost exactly like the other member of the pair. This applies to all the homologous chromosomes except one pair (which one). Use the syllabus lab web page for this exercise.
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INTERPRETATION
Now that you have finished these experiments and observations, how did your work answer the questions addressed in the Introduction? Did your offspring resemble the mother or the father? Was it intermediate between the two? Why? Did you have trouble finding a prospective parent of your Rebop among the others in the class? Summarize your answers in the space below.
BIODIVERSITY
Introduction
Life in the form of simple microbes evolved approximately 4 billion years ago. The first organisms were microbes resembling our present day bacteria. Since these early days, millions of new species have evolved creating an amazing diversity of life. Biologists have catalogued these organisms in a system of classification called the Linnean Hierarchy. Organisms are arranged in categories based on their similarities and inferred evolutionary relationships. You will spend the next two weeks studying representatives of each of the major taxonomic categories of organisms. The primary learning outcome for these two labs is for you to learn the following for each group of organisms:
1) Primary morphological characteristics of each group
2) Ecological niches these species have exploited
3) Name of the taxonomic group that these species belong to
This lab exercise has been divided up into two weeks. During Week 1 you will be studying microorganisms, Plants and Fungi. The second week will be spent learning the major groups of animals.
Outline of the lab
Survey of the major groups of organisms
Major Groups for Diversity Lab Week 1
Bacteria
Representative of Eubacteria (3 types)
Representatives of the Blue-green Algae
Protista
Various representatives
Plants
Representatives of the lower plants
Representatives of the higher plants
Fungi
Basidiomycetes
Zygomycetes
Major Groups for Diversity Lab Week 2 - Animalia
Porifera – Sponges
Cnidaria
Corals, Hydroids, Jellyfish
Platyhelminthes
Various representatives of the flatworms
Annelida
Various representatives of the segmented worms
Arthropoda
Various representatives
Echinoderms
Various representatives
Chordata
Invertebrate Chordates
Vertebrate Chordates – fish, amphibian, reptiles, birds, mammals
Student outcomes for each lab
Recognize representatives of the major groups
Know the major morphological features of each group
Know very basic ecology of each group
Diversity Lab 1
The major taxonomic groups that will be covered in this lab include the Domain - Bacteria, Domain Eukarya and the Protista, Domain Eukarya and the Kingdom Plantae and Domain Eukarya and the Kingdom Fungi. You will be studying representatives of each group by examining whole mount slides, living and or preserved specimens. Your goals are to be able to recognize each organism, know the major taxonomic group that it belongs to, some basic characteristics of the organism that is shares with other species in its taxonomic group and its ecology.
Taxonomic Group and their Representatives
Domain Bacteria
These organisms are closely related to the earliest forms of life on earth that evolved over 3.5 billion years ago. They are simple, small, prokaryotic cells with the features listed below. These organisms are found everywhere on earth and are ecologically diverse. Some species are autotrophic and capable of producing their own energy. Most species are heterotrophs and must obtain their own energy from other organisms. A summary of their ecology is listed below.
Features
Small size, lack membrane bound organelles or nucleus, simple DNA
Ecology
Mostly heterotrophic (decomposers, parasites, mutualists living inside gut of higher animals), some autotrophs – blue-green algae, chemoautotrophs
You will examine whole mount slides and living cultures listed here in Table 6-1. The bacteria are heterotrophs while the Blue-green Algae (Nostoc and Oscillatoria) are photoautotrophs.
Table 6-1. Representatives of the Bacteria.
|Representatives – slides |Representatives –living materials |Representatives - preserved materials |
|Bacteria - slides of 3 shapes – Cocci, |Bacterial colonies - E. coli | |
|Bacilli, Spirilli | | |
| | Bacterial colonies - B. megabacterium | |
| | | |
|Blue-green Algae - Nostoc | | |
|Blue-green Algae - Oscillatoria | | |
Domain Eukarya – Protista
These organisms had the first and more modern, eukaryotic cells. The earliest fossil evidence of eukaryotes dates back 1.2 billion years ago. This group contains the ancestors of the remaining Kingdoms: Fungi, Plantae, Animalia. This group is ecologically diverse. There are unicellular free-living forms and multi-cellular species. Some species, like the multi-cellular algae (seaweed) are autotrophic. The remaining heterotrophic species feed on algae or on themselves in aquatic environments and there are also some harmful, parasitic forms. The animal-like representative species for this lab were chosen to illustrate the different forms of locomotion used by some unicellular forms: pseudopod of the Amoeba, cilia of the Paramecium and flagellum of the Trypanosoma. The preserved plant-like algae are examples of multicellular forms.
Features
Large size, membrane bound organelles, complex DNA and nucleus
Ecology
Mix of autotrophs, heterotrophs, parasites, primarily aquatic (marine and freshwater)
Table 6-2 Representatives of the Protista
|Representatives – slides |Representatives –living materials |Representatives - preserved materials |
|Amoeba | |Fucus |
|Paramecium | |Ulva |
|Trypanosoma | |Red Algae |
Domain Eukarya – Bryophyta
The Bryophytes belong to the Kingdom Plantae and are probably most similar to the first plants that colonized land about 475 MYA (million years ago).
Features
No vascular tissue, no seeds, sexual reproduction by motile, swimming sperm or asexual reproduction, photosynthetic pigments, gametophyte is dominant generation, antheridium produces sperm on the male plant, archegonium produces eggs on the female plant
Ecology
All species are autotrophs that typically inhabit wet forests, streamsides and or are never found far from water because they require water for swimming sperm and fertilization.
Domain Eukarya - Pterophyta
The ancestors of this group appeared about 425 MYA and were the dominant plants on earth for the next 50 million years.
Features
Seedless vascular plants (with xylem and phloem), motile swimming sperm, sori on underside of leaf release spores for reproduction
Ecology
Similar to Bryophytes in that all species are autotrophs that typically inhabit wet forests, streamsides and or are never found far from water because they require water for swimming sperm and fertilization.
Table 6-3. Representatives of the Primitive Plants
|Domain |Group |Representatives – slides |Representatives –living or |Ecology |
| | | |preserved materials | |
|Eukarya |Plantae - Primitive Plants |Seedless plants |Photosynthetic pigments, |Autotrophs, supply oxygen and |
| | | |alternation of generations - |sugar to terrestrial ecosystems |
| | | |gametophyte (1N) and sporophyte | |
| | | |(2N) | |
| |Bryophyta - live mosses |Live mosses |Reproductive structures | |
| |Bryophyta slides |Moss - male gametophyte |Antheridium and sperm (1N) | |
| | |Moss - female gametophyte |Archegonium and eggs (1N) | |
| | |Moss - sporophyte |Stalk and sporangium (2N) | |
| |Pterophyta |Live ferns | | |
| | |Fern leaf with sori - |Sori on underside of leaf | |
| | |reproductive structure | | |
Domain Eukarya – Higher Plants
The Gymnosperms were the first of the two groups of higher plants to evolve about 360 MYA. The second group was the Angiosperms that appeared about 140 MYA. The primary adaptation of these two groups was the evolution of wind-borne pollen or sperm that freed them from being dependent on a constant water source. These plants went on to colonize all terrestrial ecosystems because they could reproduce through wind action or pollination by insects, birds and mammals.
Features
Gymnosperms
Root system, needle-leaves, reproductive cones in most species, pollen, sporophyte is the dominant generation
Angiosperms
Root system, flowers for reproductive structures, pollen, fruit, sporophyte is the dominant generation
Ecology
These plants are the primary producers of almost all terrestrial ecosystems. They play a critical role in taking CO2 out of the atmosphere. They simultaneously supply O2 that goes back into the atmosphere for all air-breathing organisms. Gymnosperms make up most of the boreal forests at higher latitudes and altitudes. Angiosperms are the dominant plants of the tropics but are also found in substantial numbers throughout the temperate and higher latitudes.
Table 6-4. Representatives of the Higher Plants
| |Plantae - advanced plants |Seed Plants | | |
| |Gymnosperms |Needle leaves and cones |Root system, pollen, needle |Primary producer in most |
| | | |leaves and cones for reproduction|terrestrial ecosystems |
| | |Pollen slide | | |
| |Angiosperms |Live flower |Root system, flowers, pollen and |Primary producer in most |
| | | |fruit |terrestrial ecosystems |
| | |Fruit examples | | |
| | |Tap root from carrot | | |
Domain Eukarya - Fungi
The oldest known fungi date back about 460 MYA. They are a diverse group of detritivores that differ from each other, primarily in their mode of reproduction.
Features
Almost all fungi have hyphae that merge together into mycelia
Zygomycetes – sexually reproduce using zygospores
Basidiomycetes – sexually reproduce using basidia and basidiospores
Ecology
These species are collectively known as detritivores. They are the decomposers that feed on dead or dying detritus, primarily on the floor of wet forests. The decomposition results in recycling important chemicals back into the forest ecosystem.
Table 6-5. Representatives of the Fungi
|Eukarya |Fungi | |Hyphae, mycelium |Detritivores - decomposers |
| |Zygomycetes |Live culture of bread mold | | |
| | |Slide of mycelia, hyphae, | | |
| | |zygospores | | |
| |Basidiomycetes |Mushroom specimens | | |
Diversity Lab 2
This lab is the second of two labs on biodiversity of life on earth. The major taxonomic groups that will be covered are members of the Animalia or animal kingdom.
Domain Eukarya - Porifera
The sponges are representatives of the Porifera. They are the simplest and most primitive group of animals. The fossil record for this group dates back about 630 MYA.
Features
Sponges are simple organisms that lack a nervous system or circulatory system. There is typically a single opening to a digestive cavity. They have flagellated cells called choanocytes that circulate fluids through the body cavity. Many species also have spicules that provide a skeletal support system.
Ecology
Most of the 9000 species are marine organisms but there are a few freshwater species. These organisms are sedentary, filter feeders.
Domain Eukarya – Cnidaria
There are three groups that form the Cnidaria or Coelenterata – Jellyfish, Hydroids and the Corals. The fossil record contains evidence of some coral-like organisms about 580 MYA.
Features
These organisms typically have a sedentary hydroid form and a mobile medusa form. The dominant stage of the life cycle of the hydroids is a sedentary hydra stage while the dominant form of the jellyfish is a mobile medusa form. The corals are sedentary and have lost the medusa stage. These species have a cnidocyte or stinging cell which is where the group gets its name.
Ecology
Most species of Cnidarians are living in shallow marine environments. The Anthozoa form the ocean’s large coral reefs. There are some freshwater hydroids. Most species are predators feeding on small plankton. Most of the coral reef species live in symbiotic relationships with algae.
Table 6-6. Representatives of the Primitive Animalia
|Domain |Group |Representatives |Features |Ecology |
|Eukarya |Animalia | | | |
| |Porifera |Preserved sponges |Single opening, choanocytes - |Sedentary filter feeders, marine |
| | | |flagellated cells and spicules - |and freshwater |
| | | |for support and protection | |
| | |Slide - spicules | | |
| |Cnidaria |Preserved jellyfish - medusa|Cnidocyte - stinging cells, |Carnivorous feeding on |
| | |stage |polyp-sedentary and asexual and |zooplankton, marine and freshwater|
| | | |medusa-mobile and sexual life | |
| | | |cycle stages | |
| | |Coral - polyp stage only | | |
| | |Live hydra demo under | | |
| | |dissecting scope | | |
| | |Slide - hydra colony (polyp | | |
| | |stage) | | |
Domain Eukarya - Mollusca
This group contains 85,000 species of clams, snails octopus and their allies. Some of the earliest fossil forms date back around 270 MYA.
Features
Most species contain an inner lining or mantle that houses the internal organs and an internal radula that is used in the physical breakdown of food (cutting and scraping). Clams and their relatives have a hard shell for an outer covering. Many terrestrial and bottom-dwelling aquatic species also contain a fleshy, muscular foot for locomotion (snails, clams). Fossils date back about 500 MYA.
Ecology
Most species are grazers feeding on algae in marine environments. There are also many marine species which are carnivores, feeding on plankton, other molluscs. Clams are sedentary filter-feeders with a diet of plankton while squid and octopi are active, swimming predators. Terrestrial snails are primarily herbivores.
Domain Eukarya - Platyhelminthes
This group is also known as the flatworms for the flat appearance of these species. Some of the earliest fossil forms date back around 270 MYA.
Features
These species are known for lacking a body cavity, circulatory and respiratory organs. The Planaria have eye-spots that cannot see but are capable of detecting light. The parasitic tapeworms are made up of proglottids which form a long chain inside the host intestine. The head or scolex of the tapeworm has a series of hooks that embed into the intestinal wall of the host.
Ecology
There are both free-living forms like the Planaria and parasitic forms like the tapeworm. The Planaria are nocturnal scavengers and predators of freshwater ponds or moist forest floors. They are also capable of self-regeneration. The tapeworms are entirely parasitic. Many species use an intermediate herbivore host before infecting humans or other carnivores.
Domain Eukarya - Annelida
These segmented worms represent an important stage in the evolution of higher animals. The division of the body into segments is considered an important step in the evolution and differentiation of other body parts (forelimbs, hindlimbs, wings, etc.) by higher animals. This group dates back about 550 MYA in the fossil record.
Features
The most important feature is segmentation of the body. They have parapodia, similar to feet for locomotion. Earthworms have one large segment called a clitellum which is used in sexual reproduction. Each earthworm is hermaphroditic, containing male and female gonads that exchange sperm and eggs at the clitellum during copulation.
Ecology
There are free-living and parasitic members of this group. You are examining a representative of the free-living forms. The earthworm plays an important role in soil aeration and fertilizing the soil with its waste. It is also prey for many species and used as fish bait. Leeches are the distant cousins of the earthworms and are blood-sucking parasites.
Table 6-7. Representatives of the Animalia: Worms
|Domain |Group |Representatives |Features |Ecology |
| |Platyhelminthes | |Flatworms, single opening to |Free-living carnivores and |
| | | |digestive system, un-segmented, |parasitic forms |
| | | |lack internal body cavity, | |
| | | |respiration through the skin | |
| | |Planaria - live culture |Eye-spots for detecting light | |
| | |Tapeworm slide |Scolex head and proglottids | |
| | | | | |
| |Annelida |Preserved earthworm |Segmented worms, clitellum for | |
| | | |reproduction | |
Domain Eukarya - Arthropoda
The Arthropoda is one of the most diverse phyla on earth. It is composed of the largest number of species and individuals with over 1.7 million described species that make up about 80% of all living species. This group dates back about 550 MYA. The segmentation of the Annelida is even more complex and highly evolved in the Arthropods with such new adaptations as wings, claws, legs, tails, etc.
Features
The name Arthropoda means jointed foot or limb that all members of this Phylum share. These organisms all possess an exoskeleton made of chitin and a cuticle or waxy covering to inhibit desication or water loss.
Ecology
The Arthropods have exploited every environment on the planet including aerial (flying forms), terrestrial, marine and freshwater ecosystems. Most species are predators feeding on other invertebrates and or small vertebrates. There are also many parasitic forms (e.g., mosquitoes and other blood-sucking insects, blowflies, ticks, lice and their relatives). The large numbers of some species are important food resources in some ecosystems. The large insect blooms in higher latitudes are primary sources of protein for birds while krill are the main source of food for whales in marine ecosystems.
Domain Eukarya - Echinodermata
This group is often considered the missing link between the invertebrates and the vertebrates. They lack a bony skeleton like invertebrates but share a very similar plan of tissue development early after fertilization with vertebrates. There are about 7000 species and this group dates back over 500 MYA in the fossil record.
Features
The group is named after a characteristic of spiny skin shared by some but not all species. The group is diverse containing the starfish, sea stars, sand dollars, sea urchins and sea cucumbers.
Ecology
Most species are found in either of two marine environments. They occupy benthic or deep water ecosystems (bottom-feeders) or shallow oceans and coral reefs (filter-feeders). Starfish are voracious predators feeding on clams and or sea stars while most other species are passive filter-feeders. Sea urchins are a favorite at sushi restaurants and boiled sea cucumbers are also an Asian delicacy.
Table 6-8. Representatives of the Animalia: Higher Invertebrates
|Domain |Group |Representatives |Features |Ecology |
| |Arthropoda | |Chitinous exoskeleton, jointed |Heterotrophs, carnivores, |
| | | |appendages, exoskeleton |parasites, freshwater, marine, |
| | | | |terrestrial and aerial forms, most|
| | | | |numerous group of organisms |
| | |Horseshoe crab shell | | |
| | |Preserved Spiders and ticks | | |
| | |Crab shells | | |
| | |Insect metamorphosis | | |
| | | | | |
| |Echinoderms | |Water vascular system, tube feet,|Benthic (bottom-dwelling) grazers |
| | | |pentaradial symmetry (5 sided), |and carnivores |
| | | |skeleton made of calcareous | |
| | | |(calcite-based) plates | |
| | |Starfish | | |
| | |Sea urchin | | |
| | |Sand dollar | | |
Domain Eukarya – Chordata (invertebrates)
Amphioxus is an invertebrate member of the Chordates. It is a member of the lancelets (Cephalochordata) who are named after their knife-shape body form. They share a basic body and developmental plan with vertebrates. They date back about 520 MYA in the fossil record.
Features
The body plan is considered to be the archetype for the vertebrates. It includes 3 features shared with the vertebrates – notochord, nerve cord and gill slits. The notochord is not made of bone but performs a similar function to the vertebrate vertebral column or backbone that protects the spinal cord.
Ecology
They are marine filter-feeders of shallow temperate and tropical seas.
Domain Eukarya – Chordata (fish)
The fish refers to a large group of cartilaginous and bony species that have fins. The evolution of the group is poorly understood but the traditional classification contains the parasitic lamprey and hagfishes, cartilaginous sharks and rays, lungfish, lobe-finned fishes and the bony fishes. Fish first appear in the fossil record about 540 MYA. The great diversification of fishes began in the Devonian period about 420 MYA.
Features
Fish have fins, lack digits and breathe through a gill system.
Ecology
They are found in all aquatic marine and fresh water environments. Most species are predators feeding on a diverse array of prey, ranging from zooplankton to small whales and seals. The lampreys and hagfishes are parasitic, attaching to and sucking blood from other fish. Commercial extinction of many species by humans is an important problem for marine ecosystems.
Domain Eukarya - Amphibia
The Amphibia descended from the lobe-finned fishes and were the first vertebrates to colonize land approximately 370 MYA. Some recent discoveries of intermediate fossil forms from Greenland have firmly established the link between lobe-finned fish and amphibians. These early fossils show the evolution of limbs from the fins of these fish-like ancestors. Most species of Amphibia are extinct and the only living representatives include the frogs and toads, salamanders and snake-like caecilians.
Features
Amphibia have true lungs but also rely heavily on breathing through their skin. Reproduction involves external fertilization in most species and young must develop through a larval stage in water.
Ecology
All species are predators with many species feeding on insect prey. Amphibians have become well known for the dramatic population declines in recent years and as ecological indicators of catastrophic damage to ecosystems. Many factors have been linked to the global decline including, habitat destruction, pollution, competition with invasive species, climate change and fungal infections by chytrids.
Table 6-9. Representative of the Animalia – Lower Chordata
|Domain |Group |Representatives |Features |Ecology |
| |Chordata | |Notochord, nerve cord and gill | |
| | | |slits | |
| | |Amphioxus preserved specimen| | |
| | |Amphioxus slide - | | |
| | |notochord, nerve cord and | | |
| | |gill slits | | |
| |Fish |Preserved fish, shark |Scales, gills, bony skeleton in |Heterotrophic herbivores and |
| | | |most forms (except sharks) |carnivores, parasites, freshwater |
| | | | |and marine forms |
| |Amphibia |Frog skeleton |Lungs, skin without scales, lay |Heterotrophic herbivores and |
| | | |unprotected eggs in water, |carnivores, always near freshwater|
| | | |alternation of generations |for reproduction |
| | | |(aquatic tadpole larva, | |
| | | |terrestrial adults), bony | |
| | | |skeleton, tetrapods (four limbs) | |
| | |Preserved frogs? | | |
Domain Eukarya- Reptilia
The first reptile descendants of the amphibian appeared about 320 MYA. The Reptilia is diverse group and contains the turtles, lizards and snakes, crocodiles and dinosaurs. Some authorities have also included birds in with reptiles because of their close evolutionary relationship with predatory dinosaurs.
Features
Except for the snakes, reptiles have 4 limbs, scales to protect the skin and prevent desication and they lay eggs. The amniotic egg of reptiles is considered to be among the most important events in vertebrate evolutionary history, freeing reptiles from a dependence on water for development and opening up exploitation to all terrestrial environments. The egg, protects the embryo from the external environments, is self-contained and has a yolk of nutrients for early embryonic development.
Ecology
This group is ecologically diverse, occupying almost all terrestrial, freshwater and marine ecosystems, except at the higher, extreme latitudes. There are herbivores and carnivores and the densest concentration is in the tropics and sub-tropics. The limited distribution is due to ectothermy or cold-bloodedness of these species.
Domain Eukarya - Aves
There are over 9000 species of birds and they first descended from carnivorous, theropod dinosaur ancestors about 150 MYA. Recent fossil discoveries of feathered dinosaurs in China have confirmed the evolutionary link between birds and carnivorous dinosaurs.
Features
The lack of teeth, hollow bones, possession of a 4-chambered heart and feathers are important characteristics of birds.
Ecology
Birds have colonized the entire planet from pole to pole and everywhere in between. There are herbivores, carnivores, carrion feeders and many species that feed on the nectar of flowering plants like our North American hummingbirds. The nectivorous birds of the tropics are critical to distributing and pollinating plants in the tropics. Some species are also known for the great migrations and migratory distances from wintering areas in the tropics to breeding areas at extreme higher latitudes. Pelagic species spend most of their lives at sea, coming back to land only to breed once every 12 – 18 months. Birds have been an important food source for humans since the Jungle fowl were first domesticated by the Chinese over 3000 years ago.
Domain Eukarya - Mammalia
The first mammals appeared about 225 MYA nearing the end of the reign of the Dinosaurs. These species were small, nocturnal insectivores known primarily from bones of the skull and mandible. The extinction of the Dinosaurs about 65 MYA lead to an explosive radiation of mammals. There are two or three groups of mammals depending on the authorities – Monotremes (not considered mammals by some biologists), Marsupials and Eutherians.
Features
The primary characteristics of mammals are the possession of hair and mammary glands. The Monotremes still lay leathery eggs. The Marsupials are named after the marsupium or pouch on the female where young complete their development. The young of Eutherian mammals complete their development inside the uterus of the female.
Ecology
Like birds, mammals have colonized the entire planet, including all major ecosystems – terrestrial, freshwater and marine. The great herds of ungulates that migrate across Africa are examples of herbivores. Bats are primarily, nocturnal insectivores but some species specialize on fruits and nectar. The big cats of Africa and Asia along with the wolves of North America and Europe are examples of predators. Whales, dolphins and seals have colonized marine habitats while otters have invaded many freshwater ecosystems in the northern and southern hemispheres.
Table 6-10. Representatives of the Animalia - Vertebrates
|Domain |Group |Representatives |Features |Ecology |
| |Reptilia |Snake skeleton |Amniote egg, lungs, bony |Heterotrophic herbivores and |
| | | |skeleton, scales, tetrapods (four|carnivores, more common in tropics|
| | | |limbs) |and sub-tropics (cold-blooded), |
| | | | |primarily terrestrial with some |
| | | | |marine and freshwater forms |
| | |Other reptile skeletons | | |
| | | | | |
| |Mammalia |Cat skeleton |Lungs, tetrapods, bony skeleton, |Heterotrophic herbivores and |
| | | |hair, mammary glands, 4 chambers |carnivores, found all over the |
| | | |heart |world, terrestrial, aerial |
| | | | |(flying), marine and freshwater |
| | | | |forms |
| | |Study skin | | |
| | |Mount | | |
| | | | | |
| |Aves |Pigeon skeleton |Lungs, tetrapods, bony skeleton, | |
| | | |feathers, 4 chambers heart | |
| | |Study skin | | |
| | |Mount - Great Horned Owl | | |
BIOLOGICAL CHEMICALS, NUTRITION AND HEALTH
Introduction
Do you eat all your greens? Are you overweight? Did you do some carbo-loading before your last marathon? Are you taking vitamin supplements? Do you have enough fiber in your diet? Do you suffer from excessive flatulence? How many times have you been asked or heard someone else ask these and other similar questions? The reason is that nutrition and diet have received a great deal of attention over the past 30 years. For instance, look at the weight control and dieting organizations that have recently appeared: Weight Watchers, Jenny Craig, Diet Workshop, Nutri/System, etc. There are always one or two cookbooks in the top ten best selling books. The general public has become extremely health conscious and one of the variables they can directly control is their diet. One of the reasons for this intense interest in diet is that research has revealed the impact of poor versus healthy diets on the quality of life of an individual, especially as he/she grows older. But how will you ever know if you are eating the right foods? What is a healthy diet?
A healthy diet is a balanced diet. The balance is between proteins, carbohydrates and fats. These are the most important organic chemicals in biology. They represent the major food groups and a proper balance of these chemicals is crucial for a healthy diet. Vitamins and minerals are some other important organic and inorganic molecules that must supplement the major food groups. Biochemists have devised some simple tests for detecting these chemicals. In Part I of this lab you will learn how to test for proteins, carbohydrates and fats in foods. You will address the following questions:
1. How do we test for different chemicals?
2. How do we test for carbohydrates, fats and proteins?
3. Why are the tests different?
Part II of this lab is an investigation of parameters of human physiology. You will take measurements of your vital signs that are indicators of cardio-vascular and respiratory health. Heart Rate or pulse is a measurement of the rate at which the heart pumps blood and oxygen out to the tissues of the body. The average resting heart rate ranges from 60 – 100 bpm. This rate is affected by many variables including the body’s physical or mental activity needs but also by gender, fitness level, body position, size, stress, ingestion, etc. Aberrations like certain heart diseases are considered to be heart rates below this range known as Bradycardia or above the range known as Tachycardia. You will measure resting heart rate and then design an experiment that could affect this rate. You will compare the resting rate with the post-experiment rate to see the effects of various activities on Heart Rate.
A second measure of cardio-vascular health is Blood Pressure which is Systolic pressure over Diastolic pressure. Systolic is typically considered maximum arterial pressure and Diastolic is considered minimum arterial pressure. The Table 7-1 below contains normal and abnormal readings of this measurement. Just like with Heart Rate, you will compare the resting rate with the post-experiment rate to see the effects of various activities on Blood Pressure.
Table 7-1 Blood pressure measurements.
|Category |Systolic |Diastolic |
|Normal |90-119 |60-79 |
|Hypotensive | ................
................
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