Procedure
Part A:
DNA Fingerprinting

You will use DNA Fingerprinting for the next two experiments.  
• First you will determine which suspect left their DNA at a crime scene.
• Then you will use it to carry out a paternity test to see who the father of a baby in question is.

Crime Scene Investigation Experiment

• The pattern created by the fragments of DNA (RFLPs) when they are cut by a restriction enzyme are as unique to an individual as a persons fingerprints (that is why it is called DNA 'fingerprinting' even though fingerprints are not involved).
• The RFLP patterns created by cutting the DNA are compared to know sizes of DNA fragments. This is called the DNA ladder.
• Look at the pattern created by the RFLPs on the gel that appears at the end of the simulation.
• The gel contains DNA collected from the crime scene and from 7 suspects. The DNA was cut using the restriction enzyme called EcoRI.
• Compare the pattern of the DNA collected at the crime scene to those collected from the 7 suspects whose DNA was also cut with EcoRI.
• The criminal would have the same RFLP pattern as the one recovered from the crime scene.
• Click on the 3 steps (after you watch the first step the second step will appear for you to watch) to set up and run the experiment to determine who left their DNA at the scene of the crime.
At the end of the 3 simulated steps for setting up and running the gel, use the gel that appears to answer the questions in Part A of Lab 5 Lab Report. If you do not complete all 3 steps for setting up and running the gel you will not be able to answer the questions about it (just like if you didn't do these steps in a face to face lab).

Click for Step 1. Set up the Gel Electrophoresis Experiment

Paternity Test

• Notice in the "Crime scene investigation gel" that some of the suspects have RFLPs in common, but only the criminal has the same exact same pattern of RFLPs as the DNA collected from the crime scene.
• In this exercise you will simulate a paternity test using DNA fingerprinting.
• Recall that everyone's DNA is unique. This means that a baby's DNA is different from both of its parents.
• However, since a baby inherits its DNA from both its parents it would also inherit the RFLP cut sites from its parents. Some of these cut sites are inherited from its mother, the rest are inherited from the father.
• Look at the DNA from the mother and the baby. Notice that the mother does not have any of the cut sites that the baby doesn't have. However, the baby has some cut sites that the mother doesn't have. The missing cut sites would have come from the father.
• To determine the father here are some rules; the father cannot have any RFLPs that the baby doesn't have (same rule applied to the mom) AND the father must provide the RFLPs that the mother didn't
• Look at the gel below to see if you can figure out who the father is.
• Answer questions in Part A of Lab 5 Lab Report.

A DNA electrophoresis gel of a paternity test showing fragments of DNAs (RFLPs) cut by restriction enzymes. The gel shows 7 lanes with RFLP bands ranging from 200 to 8000 bp. The reference DNA ladder is in the leftmost lane followed by the DNA from mother then the baby and subsequently 4 possible fathers. The following are the bands in each lane: reference DNA ladder-8000/7000/6000/5000/4000/3500/2500/2000/1500/1000/750/500/250/220/200, mother’s DNA-5000/4000/3500/2500/2000/250, baby’s DNA-5000/4000/3500/2500/2000/1500/1000/250/200, possible father 1-4000/3500/2500/2000/250, possible father 2-2500/2000/1500/1000/200, possible father 3-4000/3500/2500/2000/500, possible father 4-6000/5000/4000/3500/2500/750.

Part B:
Mendelian Traits

• Complete Table 5.1 by filling in your phenotype and genotype as answers to questions in Part B of Lab 5 Lab Report.
• Review these slides first to make sure you complete the table correctly.
• Caution - if you do not review these slide you may fill the table out incorrectly and lose points.
• Use the blue arrow to navigate to the next slide.

If you have trouble seeing the slides below click here for a different viewing option
Image highlights that the 2 possible phenotypes for the trait tongue rolling are able to roll or unable to roll.
Image highlights that you need to write your phenotype in the column “Your Phenotype”. In this example the individual can roll their tongue so they have written “Able to roll” in this column.
Image highlights that you need to write your genotype in the column called “Your Genotype”. In this example, since the individual had the dominant phenotype (able to roll) they have two possible genotypes they must write. They can be either two capital letter Rs (Homozygous dominant) or one capital R and one lowercase R (Heterozygous). You need to include both possible genotypes for the dominant phenotype.

The next slide shows how you would fill in the table if you have the recessive phenotype.

Image highlights how you would fill out the table for the trait Tongue rolling of you have the recessive phenotype. Under “Your Phenotype” is written Unable to roll and under “Your genotype” there are two lowercase letter r’s (homozygous recessive).

Now complete Table 5.1 by filling in your genotype and phenotype as answers to questions in Part B of Lab 5 Lab Report.

Here is a reminder of what each phenotype looks like. Scroll down to see Table 5.1.

The pictures illustrate some common  dominant and recessive Mendelian traits in humans. Some dominant traits are: tongue roll, freckles, widow’s peak, free earlobe, cleft chin and hitchhikers thumb. The recessive traits for the above dominant traits are: no roll, no freckles, straight hairline, attached earlobe, smooth chin and straight thumb respectively.

• Now use Table 5.1 below to answer questions 12- 27 in Lab 5 Lab Report.

Table 5.1 reads across the top 4 columns Trait, Possible alleles, Your Phenotype and Your Genotype
Row 1, under trait “Tongue rolling” Under possible alleles either able to roll (capital R) or unable to roll (lowercase r), under “Your Phenotype” is place your answer to question 12 in the lab report, under “Your Genotype” is a place for you to answer question 13 in your lab report.
Row 2, under trait “Freckles” Under possible alleles either have freckles (capital F) or no freckles (lowercase f), under “Your Phenotype” is place your answer to question 14 in the lab report, under “Your Genotype” is a place for you to answer question 15 in your lab report.
Row 3, under trait “Widow’s peak” Under possible alleles either widow’s peak (capital W) or straight (lowercase w), under “Your Phenotype” is place your answer to question 16 in the lab report, under “Your Genotype” is a place for you to answer question 17 in your lab report.
Row 4, under trait “Earlobe” Under possible alleles either free hanging (capital H) or attached (lowercase a), under “Your Phenotype” is place your answer to question 18 in the lab report, under “Your Genotype” is a place for you to answer question 19 in your lab report.
Row 5, under trait “Cleft chin” Under possible alleles either have cleft (capital C) or no cleft (lowercase c), under “Your Phenotype” is place your answer to question 20 in the lab report, under “Your Genotype” is a place for you to answer question 21 in your lab report.
Row 6, under trait “Thumb” Under possible alleles either have Hitchhikers (capital H) or straight (lowercase h), under “Your Phenotype” is place your answer to question 22 in the lab report, under “Your Genotype” is a place for you to answer question 23 in your lab report.
Row 7, under trait “Dimples” Under possible alleles either have dimples (capital D) or no dimples (lowercase d), under “Your Phenotype” is place your answer to question 24 in the lab report, under “Your Genotype” is a place for you to answer question 25 in your lab report.
Row 8, under trait “Interlocking fingers (when hands are clasped)” Under possible alleles either have Left thumb on top (capital L) or right thumb on top (lowercase l), under “Your Phenotype” is place your answer to question 26 in the lab report, under “Your Genotype” is a place for you to answer question 27 in your lab report.

Punnett Squares
• Now you are going to use YOUR genotype to answer the next set of questions in Part B of Lab 5 Lab Report.
• Let’s look an example of how to set up the Punnett squares using the freckles trait as an example in the slides below.
• If you don't look at these slides you might not answer the questions correctly or you may be confused. review these slides to help you answer these questions correctly.
• Use the blue arrow to navigate to the next slide.

If you have trouble seeing the slides below click here for a different viewing option
Image highlights that under the column for Your Phenotype in the row for the Trait “freckles” the person has written in the phenotype “Have Freckles”.
Image highlights that they have written in the genotypes two capital letter F’s (homozygous dominant) and one capital F with one lowercase F (heterozygous).
Image shows a square divided into 4 boxes. On the top of one box is a capital letter F above the second box in a lowercase letter f.

On the top I have placed the letters from the “other person” given in the lab report. These letters represent the two alleles of a gene this person is carrying. Since we inherit one allele from our mother and one from our father we always have 2 letters (2 alleles). During the process of meiosis these alleles separate.

Image shows the same boxes and letters as the previous slide with the addition of a capital letter F to the right of the upper row of two boxes and a lowercase f to the right of the lower row of two boxes.

If you have the dominate phenotype you MUST complete the Punnett square by assuming you have the heterozygote genotype (Ff). I have placed my genotype, one letter next to each box, on the side.

Image shows the same boxes and letters as the previous slide but now includes arrows showing the letters from above each box are combine with the letters to the left of each box such that the first box (which had a capital letter F above it and to the left of it now reads  FF (two capital letter F’s) and the box to the right of that (which had a lowercase f above it and a capital F to the left) now reads capital F lowercase f.

Now we can fill in the 4 squares of the Punnett square to see what phenotypes and genotypes the offspring from this mating could have. Follow the arrows to see how I filled in the top two squares

Image shows the same boxes and letters as the previous slide. There are now arrows showing the lower row of boxes being filled in. The lower left-hand box (which had a capital F above it and a lowercase f to the left) now reads capital F lowercase f. the box to the right of that (which had a lowercase f both above it and to its left) now reads two lowercase f’s.

Follow the arrows to see how I filled in the bottom two squares.

The next slide shows how you would set up the Punnett Square if you have the recessive phenotype.
NOTE - The other person's genotype , which you are given, has not changed.

Image shows what the Punnett square will look like if the person has the recessive phenotype of no freckles. The same two given letters of capital F and lowercase f are on top. The persons genotype of two lowercase f’s appears on the left-hand side with a single lowercase f next to each box. When the boxes are filled in the upper left-hand box now reads capital F lowercase f. The upper right-hand box reads two lowercase f’s. The lower left hand box reads capital F lowercase f and the lower right-hand box reads two lowercase f’s.

This is what the Punnett square will look if you have the recessive phenotype.

When you are asked for the phenotypes there are always only 2 possible phenotypes (freckles or no freckles). Any box you filled in that has at least 1 capital letter “F” has the dominate phenotype (freckles) and boxes that only have a lower case "f” (ff) have the recessive phenotype (no freckles).

So, for the Punnett square using the dominate phenotype 75% (3 of the 4 boxes) have freckles (because they have the genotypes FF or Ff) and 25% (1 of the four boxes) have no freckles (because they have the genotype ff).
When we used the recessive phenotype 50% have freckles (Ff) and 50% have no freckles (ff).

Now use Punnett Squares to estimate the inheritance given when YOU and another person are crossed for the traits specified in Lab 5 Lab Report.
Answer questions in Part B of Lab 5 Lab Report.

Part C:
Fertilization of Sea Urchin eggs

• Use the images on these slides to answer questions in Part C of your Lab Report.
• The first slide shows freshly spawned eggs before a drop of sperm is added.
Look back on the "Sea Urchin eggs"section to help you distinguish the mature eggs from the immature eggs and the unfertilized eggs from the fertilized eggs.
• The second slide shows the same eggs after a drop of sperm has been added.
• Use the black arrow to navigate to the slide of fertilized eggs

The image shows a total of 16 freshly spawned sea urchin eggs released in the water. Some of the eggs in the picture are immature but others are mature. 7 out of 16 eggs have a large  nucleus and 9 lack have a very small nucleus.
The image shows the same 16 sea urchin eggs as the previous slide after the addition of sperm. Some of the eggs in the picture are fertilized but others aren't. 7 out of 16 eggs still have a large nucleus. 9 appear to be surrounded by a halo.

After you have submitted your Lab Report Via Google please go to Blackboard, select the Lab for this week and the "Grading Rubric" . Then select "Write Submission" and type in "I have submitted my Lab Report Via Google docs"
This will allow me to enter a grade that you can see on Blackboard in your grade book for each lab.

Non-majors College Biology Lab Manual © 2021 by Marie McGovern Ph.D. is licensed under CC BY-NC 4.0