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UCSD The Microscope and The Cell Lab

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Part 1 – Cell size

The cell is the fundamental unit of life and all living things are made of cells. What determines the size of a cell? This lab will investigate why cells have a upper and lower limit on size. 


  1. Read OpenStax section 4.2 (Links to an external site.) (Visual Connection) for a brief discussion of cell size.
  2. Determine the Rationale for Optimum Cell Size
    1. Have you ever wondered why cell are so small? Or why they aren’t bigger? What is the biggest (or smallest) a cell can be?
    2. Consider the diagram below and discuss with the class the limits on cells size
      • Cells of two different sizes, 1 mm vs. 2 mm
  3. Modelling Surface Area to Volume
    1. Scientists often use models as a conceptual representation of how a biological system might work. Some models assume the cell is shaped like a cube (like the model in the video and in your textbook) and some models assume the cell is shaped like a sphere (like the model in the simulation below). The reality is that cells come in all different shapes: some are spheres, some are rods, some are cube shaped, while some are asymmetrical.
    2. Whatever the shape of the cell, the cell’s membrane serves as the boundary between the inside of the cell and the outside of the cell. The membrane allows materials like carbon dioxide and oxygen to flow in and out of the cell. Small molecules like CO2 and O2 move into and out of the cell by a process called diffusion. As you will learn in this course, diffusion is the passive movement of particles from high concentration to low concentration. Let’s focus on the diffusion of CO2. Carbon dioxide is a waste product in animal cells; it must diffuse out of the cell so it can eventually move to our lungs and be removed from our body by breathing. If CO2 builds up in our cells, our cells can’t function as well and the cell could fail and “die.” 
    3. Here is the question we will attemt to solve: how does the size of the cell influence the ability of CO2 to leave the cell? We will attempt to solve this question by looking at a model of how diffusion works based on the radius of the cell. 
    4. Before you run the simulation, familiarize yourself with how the simulation works:
      • The cell diffusion simulator
      • X-You can ignore these tabs, we don’t need them.
        1. You can set the radius of your cell here by sliding the toggle from 0 LaTeX: mum -100 LaTeX: mum. Remember, LaTeX: mum stands for microns or micrometers. Radius is the distance from the center of the sphere to the edge. 
        2. This simulation will automatically calculate the surface area of your cell in square microns (LaTeX: mum2). If you want to do the math yourself, the surface area, SA, is SA = 4LaTeX: pir2
        3. This simulation will automatically calculate the surface area of your cell in cubic microns (LaTeX: mum3). If you want to do the math yourself, the volume, V, is V = 4/3LaTeX: pir3
        4. This simulation will automatically calcuate the surface area to volume ratio of your cell. This measurement demonstrates a relationship between how much surface area the cell has (the cell membrane) and the volume (the cell contents like cytoplasm, mitocondria, nucleus, etc) it contains. If you want to do the math yourself, the surface area to volume, is simply the surface area divided by the volume, SA/V
        5. After you have set the radius you want to model, you hit Run and the simulation will graph the data.
        6. If you want to clear your runs, hit Reset.
        7. A graphical representation of how big your cell is.
        8. This graph shows how fast materials (like CO2) can move out of the cell based on the cell’s size. Let’s look at each part of the graph:
          1. The Y axis depicts the concentration of CO2 inside the cell at time zero (the beginning). Note that at the beginning the concentration of CO2 is 1M. If you are unfamiliar with units of molarity (M), that’s ok! You will learn it in chemistry; all you need to know is that it is a unit of concentration: the higher the number, the more concentrated it is. 
          2. The X axis depicts time in seconds. Note the simulation ends at 12 seconds. 

Let’s try a practice run. Set the radius to 100 microns and click run. Do you see how the molarity of CO2 goes from 1M at T = 0 seconds to (approximately) 0.85 M at T =12 seconds? This means the concentration of CO2 decreased from 1M to 0.85M over the span of 12 seconds. 

Now let’s run the simulation. You will run the simulation 6 times with the following radius values: 10, 20, 40, 60, 80, 100 LaTeX: mum. For each radius make note of the surface area to volume ratio  and the molarity of CO2 at 12 seconds. Your data table should look something like this:

Cell radius, surface area, and rate of diffusion

Radius of Cell (LaTeX: mum)

Surface Area to VolumeMolarity of CO2 at 12 seconds1020406080100

Now that you have your data, you will make two scatterplot graphs and enter them in the Lab02 ELN. 

  1. Make a scatter plot that compares the radius of a cell to its SA/V ratio. The radius of the cell is the independent variable; the SA/V is the dependent variable. You can either make a graph in Google Sheets or sketch it on paper. Paste this graph into the Lab 04 ELN. Determine the correlation between these two variables: is it positive? negative? no correlation?
  2. Make a scatter plot that compares the radius of a cell to the Molarity of CO2. The radius of the cell is the independent variable; the Molarity of CO2 is the dependent variable. You can either make a graph in Google Sheets or sketch it on paper. Paste this graph into the Lab 04 ELN. Determine the correlation between these two variables: it is positive? negative? no correlation?

These two graphs should help you understand the relationship between the size of the cell (the radius) and how fast waste products (CO2) can leave the cell through the surface (cell membrane). Ask yourself: As the cell gets bigger, how does it’s ability to exchange materials across the cell membrane change? 

Part 2 – Using a microscope

The cell is the fundamental unit of life, but how did scientist first discover them? Almost all cells are too small to see with the naked eye. The invention of the microscope revolutionized the study of life and made the invisible world visible. The microscope is an instrument that allows scientists to view very small things in detail. Scientists can view the shape of very small organisms, see some details of their anatomy, and estimate the size of the organism or the organism’s features. This lab will investigate how microscopes work and how scientists can use them. 

1. Introduction to Microscopy

In this lab, you learn the theory and basic use of a compound light microscope. Recall what it is like to use a magnifying glass, as the light passes through the lens, the lens bends the light so that you see a magnified image. Early microscopes were simple light microscopes because they only had one lens; they were a small magnifying glass over a stage on which the specimen was placed:

The microscope use by Antonie van Leeuwenhoek

The first man to see a microbe (Links to an external site.)

Most scientists today use compound microscopes. “Compound” refers to the fact that an object is viewed through two lenses, the ocular and objective lenses. The eyepiece contains the ocular lens, which magnifies the specimen. By rotating the nosepiece you can select one of the three objective lenses, which typically have magnifications of 4×, 10×, and 40×. Total magnification is calculated as a product of the two lenses. A microscope slide is placed on the stage, which has an opening for light to pass through. The slide is held in place by a mechanical stage with stage clips. Light is supplied by a built in microscope lamp. The light source is then concentrated by a condenser, which can then be adjusted by the iris diaphragm. Coarse and fine focus knobs allow you to bring the object into clear focus.

The microscope and its parts

Part 2 – Using the virtual microscope

Now it’s your turn! Practice using a virtual microscope by clicking on the link below. Follow the directions to explore the specific activities in this simulation: Virtual Microscope.

To complete this simulation

  1. Click on Guide

Guide to the virtual microscope

  • Click through the Introduction, Overview, Objective lenses, Immersion Oil Lens, and Microscope Care guides. Be sure to click through and read each page of each module.

Learn the virtual microscope

  1. Click on Learn and quiz yourself on the different parts of the microscope

Quiz yourself on the virtual microscope

  1. Click on Explore and observe the following slides

Explore images with the virtual microscope

  • Plant Slides 
    • Plant Cell – include in ELN
    • Onion Root – include in ELN
  • Animal Slides
    • Spider
    • Spider Leg – include in ELN
  • Bacteria Slides
  • Human Slides
    • Blood
    • Columnar Epithelial Cells – include in ELN
    • Cuboidal Epithelial Cells – include in ELN
  1. Be sure to sketch each microscope view as best you can, and paste the indicated sketches into the Lab 02 ELN. Drawings are difficult in electronic documents. Draw them by hand, take a picture, and paste into the google doc. While I’m not asking you to put all the microscopic images into your notebook, you should also sketch the others. You will need them for the quiz.


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