BIO 101 BU Microscopy and Taxonomy Lab Report

Taxonomy
Name:
Introduction
Because the diversity of life on Earth is so vast, biologists use a general system of classification and
naming organisms (taxonomy) to track and organize species based on evolutionary relatedness. The
broadest taxon is the domain; organisms belong to one of the three domains (Bacteria, Archaea, and
Eukarya). Within the domains are increasingly specific taxa, usually following the order in the table
below.
The scientific name of an organism is given using binomial nomenclature; the genus and species of an
organism give its specific scientific name. These names are usually derived from Greek or Latin, and
therefore must be italicized when written. The genus is to be capitalized and the species is lower case.
For example, the scientific name of a common wombat (top) is Vombatus ursinus.
Let us compare the wombat to a similar species, a quokka (bottom).
Wombat
Quokka
Domain
Eukarya
Eukarya
Kingdom
Animalia
Animalia
Phylum
Chordata
Chordata
Class
Mammalia (Marsupialia)
Mammalia (Marsupialia)
Order
Diprotodontia
Diprotodontia
Family
Vombatidae
Macropodidae
Harrison (jjharrison89@facebook.com) – Own work.
Genus
Vombatus
Setonix
Licensed under CC BY-SA 3.0 via Wikimedia Commons
Species
ursinus
brachyurus
“Vombatus ursinus -Maria Island National Park” by JJ
Note that both animals differ only when we reach the family level. If you knew that a
kangaroo was in the same family as a quokka, would you assume the quokka was more
closely related to a kangaroo or a wombat?
Scientific names might seem confusing, but are useful for several reasons. Common
names tend to vary according to region (crawfish, crayfish, mudbug, crawdad), but the
scientific name is always the same.
Questions:
“Quokka” by the Hotel Rottnest, WA, Rottnest
Island” by Vicsandtheworld – Own work. Licensed
under CC BY-SA 3.0 via Wikimedia Commons
1. Llamas, alpacas, and camels are all in the same family: Camelidae.
Therefore, it is reasonable to assume that these animals will also be in the same…
2.
The scientific name of the brown-throated three-toed sloth is named Bradypus variegatus. What is
the genus of the organism? The species?
Part 1: A Simple Dichotomous Key
A dichotomous key is a tool used to determine the identity of species that have been previously
described. You can think of it as a series of questions in which each question only has two possible
answers.
In the table below, you have been given a list of creatures and their descriptions. The different
characteristics, behaviors, and habitats of the creatures can be used in the dichotomous key to
differentiate among them.
Creature
Jackelope
Chupacabra
Altamaha-ha
Sasquatch
Yeti
Kraken
Nessie
Description
Mean-spirited horned jack rabbit
Reptilian creature covered in scales with spines along the dorsal
ridge; likes to eat goats
Water monster with an alligator-like head and long neck; lives in the
marshes of Coastal Georgia
Stinky giant humanoid covered in brown fur; found in the forests of
North America
Giant mountain humanoid covered in white fur; prefers the snow
Giant octopus-like creature; takes down ships in the open ocean
Water monster with a snake-like head and long neck; lives in Loch
Ness, in the Scottish highlands
Below, you will find the dichotomous key used to identify a folkloric creature you may come across. On
the left is the list of questions and on the right, the same list is represented as a flowchart. Both are
useful representations of the same dichotomous key.
1.
2.
3.
4.
5.
6.
Does the creature live on land?
a. Yes: go to question 2
b. No: go to question 5
Does the creature resemble a human?
a. Yes: go to question 3
b. No: go to question 4
Does the creature have brown fur?
a. Yes: Sasquatch!
b. No: Yeti!
Does the creature have scales?
a. Yes: Chupacabra!
b. No: Jackelope!
Does the creature have tentacles?
a. Yes: Kraken!
b. No: go to question 6
Does the creature have a large head, resembling an alligator?
a. Yes: Altamaha-ha!
b. No: Nessie!
Using the dichotomous key, identify the creature at
right.
“Patterson-Gimlin film frame 352″ by
Patterson-Gimlin film. Via Wikipedia
Part 2: Building a Dichotomous Key
In the table below, there are several different emojis. Your job is to build a dichotomous key that would
help distinguish among them. There is space in the table to write out a description of each emoji, if
necessary, as well as a name for each. Record your question series in the space below.
Emoji
Description
Dichotomous Key Questions:
1.
a.
b.
2.
a.
b.
3.
a.
b.
4.
a.
b.
5.
a.
b.
Name
Microscopy
(Adapted from
http://www.biologycorner.com/)
Introduction
A microscope is an instrument that magnifies an object so that it may be seen by the observer. Because
cells are usually too small to see with the naked eye, a microscope is an essential tool in the field of
biology. In addition to magnification, microscopes also provide resolution, which is the ability to
distinguish two nearby objects as separate. A combination of magnification and resolution is necessary
to clearly view specimens under the microscope. The light microscope bends a beam of light at the
specimen using a series of lenses to provide a clear image of the specimen to the observer.
In this lab, parts of the microscope will be reviewed. Students will learn proper use and care of the
microscope and observe samples from pond water.
Parts of the microscope
Magnification
Your microscope has 4 objective lenses: Scanning (4x), Low (10x), High (40x), and Oil Immersion (100x).
In this lab you will not use the oil immersion lens; it is for viewing microorganisms and requires technical
instructions not covered in this procedure.
In addition to the objective lenses, the ocular lens (eyepiece) has a magnification. The total
magnification is determined by multiplying the magnification of the ocular and objective lenses.
Magnification
Ocular lens
Total Magnification
Scanning
4x
10x
40x
Low Power
10x
10x
100x
High Power
40x
10x
400x
Oil Immersion
100x
10x
1000x
General Procedures
1.
Make sure all backpacks, purses, etc. are off the benchtop.
2.
Carry microscope by the base and arm with both hands.
3.
Store with cord wrapped around microscope and the scanning objective clicked into place.
Focusing Specimens
1. Plug your microscope in to power supply and switch on illuminator.
2. Always start with the stage as low as possible and using scanning objective (4x). Odds are, you will
be able to see something on this setting (sometimes it’s only a color). Use the coarse knob to focus:
the image may be small at this magnification, but you won’t be able to find it on the higher powers
without this first step. Move the mechanical stage until your focused image is also centered.
3.
Once you’ve focused using the scanning objective, switch to the low power objective (10x). Use the
coarse knob to refocus and move the mechanical stage to re-center your image. Again, if you
haven’t focused on this level, you will not be able to move to the next level.
4.
Now switch to the high power objective (40x). At this point, ONLY use the fine adjustment knob to
focus specimens.
5.
If the specimen is too light or too dark, try adjusting the diaphragm.
Cleanup
1.
Store microscope with the scanning objective in place and the stage in its lowest position.
2. Wrap cords around microscope.
3. Replace slides to original slide tray.
Troubleshooting
Occasionally you may have trouble with working your microscope. Here are some common problems
and solutions.
1.
Image is too dark!
2.
There’s a spot in my viewing field- even when I move the slide the spot stays in the same place!
•
•
Adjust the diaphragm, make sure your light is on.
Your lens is dirty. Use lens paper, and only lens paper to carefully clean the objective and ocular
lens. The ocular lens can be removed to clean the inside.
3.
I can’t see anything under high power!
•
Remember the steps, if you can’t focus under scanning and then low power, you won’t be able
to focus anything under high power.
4.
Only half of my viewing field is lit, it looks like there’s a half-moon in there!
•
You probably don’t have your objective fully clicked into place.
5.
I see my eyelashes!
6.
This is giving me a headache!
•
•
You’re too close to the objectives. Move your head back a little.
Relax. Try adjusting the ocular distance, check that the intensity of your light isn’t too high or
too low. Take breaks if needed!
BE PATIENT AND KEEP TRYING. USING A MICROSCOPE TAKES PRACTICE!!
Part 1: Orientation of Images in the Microscope
A large part of the learning process of microscopy is getting used to the orientation of images viewed
through the oculars as opposed to with the naked eye. A common mistake is moving the mechanical
stage the wrong way to find the specimen. This procedure is merely practice designed to make new
users more comfortable with using the microscope.
Materials
•
Compound microscope
•
Microscope slide with the letter ” e ”
Procedure
1. Place the letter ” e ” slide onto the mechanical stage. Be sure to note the orientation of the letter
” e ” as it appears to your naked eye.
2.
Use the SCANNING (4x) objective and course focus adjustment to focus, then move the
mechanical stage around to find the letter ” e ” . Note the orientation when viewed through the
oculars.
Does the lens of the microscope reverse the image?
Does it flip the image? (upside down)
Part 2: Practice with Depth of Field in the Microscope
This portion of the procedure is another practice to demonstrate depth perception. Many new
microscope users find it difficult to conceive that the specimen on the slide is in three dimensions. As
the stage is moved up and down, different threads will be in focus.
Materials
•
Compound microscope
•
Microscope slide with 3 threads
Procedure
1. Place the thread slide onto the mechanical stage.
2.
Use the SCANNING (4x) objective and course focus adjustment to focus, then move the
mechanical stage around to find the threads.
3.
If needed, switch to the low power (10x) objective and refocus.
4.
Determine which thread is on the bottom, middle, and top of the slide.
TOP
MIDDLE
BOTTOM
Part 3: Investigation of Pond Water & Microorganisms
Materials
•
Compound microscope
•
Microscope slide
•
Coverslip
•
Transfer pipette
•
Pond water sample
Procedure
1. Using the transfer pipette, transfer a drop of pond water onto a microscope slide. The best
specimens usually come from the bottom and probably will contain chunks of algae or other
debris that you can see with your naked eye.
2.
Place coverslip onto the slide.
3.
Use the SCANNING (4x) objective to focus, then move the mechanical stage around to scan the
slide for live microorganisms. You are looking for tiny swimming beings- they may look green or
clear and might be very small. Choose one to focus on and center it in your visual field.
You may wish to use the ProtoSlo to keep your organisms from swimming to quickly!
4.
Switch to low power (10x). This may be sufficient to view your chosen organism. Try to note how
it moves and do your best to draw it as you see it, unless you need more magnification.
5.
Once you have centered and focused the image, switch to high power (40x) and refocus. Note
movements and draw the organism as you see it.
Remember, do NOT use the coarse adjustment knob at this point!
Questions:
1. Why is it important to begin focusing with the scanning objective?
2.
If you’re using the 40X objective and you know your ocular is 10X, what is the total
magnification?
3.
If you bump your microscope and lose focus, what do you do to refocus your specimen?
4.
Why must you center your image before switching to a higher objective?
Parts of the Cell
Introduction
The cell theory states that all living things are composed of cells, cells are the basic units of life, and that all cells
arise from existing cells. In this course, we closely study cells. There are 2 types of cells: prokaryotic and
eukaryotic. Prokaryotes lack a nucleus and true organelles, and are typically significantly smaller than eukaryotic
cells. Prokaryotic organisms are found within the domains Bacteria and Archaea. Eukaryotic cells do contain
nuclei, as well as other organelles that work together to support homeostasis of the whole cell. Though
eukaryotes are larger than prokaryotes, we must use a microscope to view all cells, which are typically too small
to see with the naked eye.
There are vast differences between cell types, but a few features are common to all cells: plasma membrane,
cytoplasm, ribosomes, and cytoskeleton. All cells also use DNA for their genetic material; in eukaryotes this is
within the nucleus and in prokaryotes it is found in the nucleoid region of the cytoplasm. Prokaryotes generally
have a cell wall made of peptidoglycan and some have flagella or fimbriae, which are used for movement or
attachment. Eukaryotes have several more organelles and are further differentiated into 2 categories: plant cells
and animal cells.
Some organelles common to eukaryotes include mitochondria, peroxisomes, vesicles, lysosomes, smooth and
rough endoplasmic reticula, and Golgi bodies. Animal cells tend to lack cell walls and chloroplasts, while plant
cells do contain chloroplasts and have cellulose cell walls.
In this lab, bacterial, animal, and plant cells will be observed using the microscope. Students will draw what was
visualized to record their observations.
Part 1: Bacterial Cell
View a prepared slide of common bacterial cell types; prepare a wet mount of cyanobacteria and observe under
the microscope.
Materials
•
Compound microscope
•
Methylene blue
•
Microscope slide
•
Cover slip
•
Transfer pipette
•
Culture of Oscillatoria
Procedure
A. Fixed slide of bacterial types
1.
Examine the demonstration slide of mixed bacteria. There are 3 common shapes:
round (coccus), rod (bacillus), and spiral (spirillum). The slide should have several
of each type of bacteria.
2.
Draw each of the bacterial shapes in the spaces at right.
B. Wet mount of Oscillatora
1.
Using the transfer pipette, transfer a drop of liquid culture onto a microscope slide.
2.
Place coverslip onto the slide.
3.
Use the SCANNING (4x) objective to focus. You are looking for very faint green thin filaments.
4.
Switch to low power (10x). You may be able to see lines going across the filaments, but the image will
likely just look like green floss.
5.
Once you have centered and focused the image, switch to high power (40x) and refocus. The individual
cells should be visible at this magnification; each filament is composed of cells stacked on top of each
other.
Remember, do NOT use the coarse adjustment knob at this point!
6.
Sketch the bacteria at low and high power. Label the cytoplasm and cell wall of a single cell. Draw your
cells to scale.
Questions:
1. Why are nuclei not visible within the cells viewed?
2. The common name for species like Oscillatoria is blue-green algae. This group of bacteria are capable of
photosynthesizing. Do they contain chloroplasts? Explain.
Part 2: Animal Cell
Prepare a wet mount of a human cheek cell and observe
under the microscope
Materials
Compound microscope
Methylene blue
Microscope slide
Cover slip
Toothpick
Procedure:
1.
Put a drop of methylene blue on the slide.
2.
Gently scrape the inside of your cheek with the flat
side of a toothpick. Scrape lightly!
Figure 1: Human cheek cell stain at high power
“Cheek Cells Identified (400x)” by biologycorner, via Flickr
3.
Stir the end of the toothpick in the stain and throw
the toothpick away.
4.
Place a coverslip onto the slide.
5.
Use the SCANNING (4x) objective to focus. You probably will not see the cells at this power.
6.
Switch to low power (10x). Cells should be visible, but they will be small and look like nearly clear
purplish blobs. If you are looking at something very dark purple, it is probably not a cell.
7.
Once you think you have located a cell, switch to high power (40x) and refocus.
Remember, do NOT use the coarse adjustment knob at this point!
8.
Sketch the cell at low and high power. Label the nucleus, cytoplasm, and cell membrane of a single cell.
Draw your cells to scale.
Questions
1. Why is methylene blue added?
2.
3.
4.
The light microscope used in the lab is not powerful enough to view other organelles in the cheek cell.
a.
What parts of the cell were visible?
b.
List 2 organelles that were NOT visible but should have been in the cheek cell.
Is the cheek cell a eukaryote or prokaryote? How do you know?
Keeping in mind that the mouth is the first site of chemical digestion in a human. Your saliva starts the
process of breaking down the food you eat. Keeping this in mind, what organelle do you think would be
numerous inside the cells of your mouth?
Part 3: Plant cells
Prepare wet mounts of an onion cell and an Elodea leaf cell and observe both under the microscope
Materials
•
Compound microscope
•
Microscope slide
•
Cover slip
•
Dropper bottle with dH2O
• Forceps
•
Pre-cut onion bulb
•
Culture of Elodea
•
Dissecting needle
Procedure
A. Wet mount of an onion cell
1.
Put a drop of water onto the microscope slide.
2.
Using the forceps, gently peel off a small piece
of the “membrane” of the onion (epidermis). It
should be very thin and may curl up on itself.
Figure 2: Onion cells at high power
“Onion 100x” by biologycorner, via Flickr
3.
Place the onion sample into the drop of water on your
slide. Try to unroll/straighten out the sample to view a single layer of cells. You may need to use the
dissecting needle to do this.
4.
Place a coverslip onto the slide.
5.
Use the SCANNING (4x) objective to focus. You probably will not see the cells at this power.
6.
Switch to low power (10x). Cells walls should be visible: they will look like semi-clear grid lines.
7.
Once you think you have located a cell, switch to high power (40x) and refocus.
8.
Sketch the cell at low and high power. Label the nucleus, cytoplasm, and cell wall of a single cell. Draw
your cells to scale.
B. Wet mount of an Elodea leaf cell
1.
Put a drop of water onto the microscope slide.
2.
Using the forceps, gently tear off a small piece of a leaf from Elodea.
3.
Place the Elodea leaf into the drop of water on your slide.
4.
Place a coverslip onto the slide.
5.
Use the SCANNING (4x) objective to focus. You probably will not see
the cells at this power.
6.
Switch to low power (10x). Cells walls should be visible: they will
look like dark grid lines.
7.
Once you think you have located a cell, switch to high power
(40x) and refocus.
8.
Sketch the cell at low and high power. Label the chloroplasts,
cytoplasm, and cell wall of a single cell. The nucleus may be
visible as well- it will be a large, clear figure. Draw your cells to
scale.
Figure 3: Elodea cells at low power
“Anacharis 40x” by biologycorner, via Flickr
Figure 4: Elodea cells at high power
“Anacharis 400x” by biologycorner, via Flickr
Questions
1.
Describe the shape and the location of chloroplasts.
2.
Were chloroplasts observed in the onion cells? Why or why not?
3.
Is this statement true or false? “Animal cells have mitochondria; plant cells have chloroplasts.”
Explain.
4.
Fill out the Venn diagram below to show the differences and similarities between the onion cells
and the Elodea cells.

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