Describe the process of DNA Profiling.

Purpose
This assignment should help you connect the concepts from Module 4 (Heredity) and Module 5 (Molecular Genetics & Biotechnology).
Objectives
⦁ After completing this activity you should be able to:
⦁ Describe the process of DNA Profiling.
⦁ Describe the role of mutation in the origin of the DNA variations that provide the basis for DNA profiling.
⦁ Explain the role of the Polymerase Chain Reaction in DNA Profiling.
⦁ Apply your understanding of meiosis to create appropriate chromosome combinations for gametes to produce the genetic make up of a baby for the profile activity.
⦁ Explain how the rules of chance are applied to determining the probability that two DNA samples come from the same individual.
Introduction
Paternity case for the child of Anna Nicole Smith
In September of 2006 Anna Nicole Smith gave birth to a baby girl, Dannielynn. After Anna Nicole’s death in February 2007 several men came forward claiming to be the father of Dannielynn. To settle the dispute and determine who the father of the child actually is, a judge ordered DNA tests for the two most likely contestants, Howard K. Stern, Anna Nicole’s personal attorney, and Larry Birkhead, her former boyfriend.
In this activity you will analyze fictional DNA data in a simulated DNA profile to determine who is the father of Danielynn. You will be presented with the DNA profiles of Anna Nicole, Howard K. Stern, and Larry Birkhead. You will use the DNA/chromosome information for Anna Nicole and the real father to “make a baby” – or at least the DNA data for baby Dannielynn and then compare the baby’s DNA profile to the three possible parents to determine who is the father of the child you created.
First, let’s take another look at DNA profiling before jumping into the profiling activity.
How DNA Profiling Works
DNA profiling, also called DNA fingerprinting, makes use of segments of DNA that do not code for protein products, but do exhibit variability (caused by mutation) in the nucleotide base sequences from individual to individual. Because these particular sections of DNA are not involved in making important protein molecules, mutations have no affect on the health or survival of the individual. This means that any mutations that occur just hang about in our DNA and are passed from generation to generation and are not selected out of the population like a deleterious mutation in an important gene would be. The segments of DNA being investigated contain mutations that have produced varying numbers of repeated letters from one individual to another, like a molecular stutter. One segment of DNA on chromosome #5 that is routinely used in DNA profiling includes from 7 to 16 repeated sequences of the short sequence, AGAT.
DNA profiling for humans is a highly standardized process. The FBI has set the standard and routinely uses 13 specific DNA locations on chromosomes 2, 3, 4, 5 (2 loci), 7, 8, 11, 12, 13 16, 18, and 21, in addition to the sex chromosomes.
Each person inherits two versions of these variable length DNA segments on their chromosomes, one from the person’s father and one from the mother.
In DNA profiling, these segments of DNA are amplified using polymerase chain reaction (PCR), to produce millions of copies of the 28 types of DNA fragments of various lengths that are unique to each individual. There is one type of fragment from each of the 13 loci from the paternal chromosomes and 13 from the maternal chromosomes, plus the two sex chromosomes. A person might inherit chromosome #5 from her mother that has 7 repeated copies of the AGAT section and a #5 chromosome from her father that has 10 repeats, or any two combinations of the 7-16 repeats.
Special single-stranded DNA primers that initiate DNA replication just upstream and downstream from the specific DNA fragments insure that only the desired segments of DNA are amplified. Each primer is about 25 nucleotides long. One of the two primers for each locus is “visually tagged” with a colored, fluorescent molecule that helps locate that DNA segment during the analysis of the amplified samples.
After the DNA segments from a sample of DNA from a person are amplified and “tagged” with the colored primers they are “loaded” onto a gel electrophoresis apparatus and separated by length. An electric current passed through a porous gel causes the negatively charged DNA fragments to move through the gel toward the positive electrode. Smaller fragments move rapidly. Longer fragments are impeded by the gel.
Animations
Electrophoresis Animation
Electrophoresis animation from DNA Interactive
⦁ Select “Techniques at the bottom of the screen
⦁ Select “Sorting and Sequencing” from the top of the next screen
⦁ Select the “Gel Electrophoresis” animation
The DNA fragments are scanned by a laser probe as they pass through the electrophoresis gel. The fluorescent, colored primers attached to each fragment are detected as they pass the laser probe. Because each person has a different combination of DNA fragments of varying length, the pattern of colors detected by the laser probe is different for each person.
Watch this animation to get an excellent explanation of the process of DNA Profiling. See the animations on Polymerase Chain Reaction below if you want a refresher on PCR.
New Methods of DNA Profiling using PCR and STRs (Short Tandem Repeats). DNA Interactive: Applications
⦁ Select “Human Identification from the bottom of the first screen
⦁ Select “profiling” from the top of the second screen
⦁ Roll your mouse over the right hand circle near the top of the screen (“Today’s DNA Profile”) and click to select the animation
Review of Polymerase Chain Reaction
Animation of the Polymerase Chain Reaction from sumanasinc.com
⦁ Select “The Polymerase Chain Reaction (PCR) ”
Polymerase Chain Reaction from DNA Interactive
⦁ Choose “Techniques” at the bottom of the next screen
⦁ Choose “Amplifying” at the top of the next screen
⦁ Two animations, “Making many copies of DNA” and “PCR animation” are very useful
DNA Profiling Activity – Paternity Case
Before starting this activity, watch the DNA Profiling animation – New Methods of DNA Profiling using PCR and STRs (Short Tandem Repeats). If you do not, there is a high probability of confusion and frustration.
To complete this activity, download or cut and paste the Module 5 Assignment Template. Follow the directions to make a baby, complete the electrophoresis gel table, determine the parents of your baby, and finally, answer the questions that follow the table. You may re-submit your assignment file as many times as you like until the due date.
In this activity, only four of the 13 DNA loci used by the FBI for DNA profiling were chosen to simulate the DNA profiles of Anna Nicole Smith and the two self-professed fathers of her baby girl. The four DNA loci are designated by the codes used by the FBI. The colors noted indicate the color of the fluorescent PCR primer used to amplify that section of DNA.
⦁ Chromosome #2 – “⦁ TPOX” – Yellow
⦁ Chromosome #5 – “⦁ D5 S818” – Red
⦁ Chromosome #7 – “⦁ D7 S820” – Blue
⦁ Chromosome #13 – “⦁ D13 S317” – Green
The electrophoresis gel table in the Module 5 Assignment Template is a simulated electrophoresis gel that indicates the relative positions of the various length DNA fragments from the three possible parents. Gel electrophoresis separates DNA fragments based on their length.
Each sample is designated by a letter, so the person performing the DNA analysis will not know which sample belongs to which subject.
As the negatively charged DNA fragments are pulled toward the positive electrode at the bottom of the gel, the shorter fragments move faster and the longer fragments are impeded by the fibrous nature of the gel. In a real world profile, the DNA fragments would continue to move through the gel and pass a laser source and detector that would record the colored flash of light emitted by the fluorescent primer attached to each DNA fragment (see DNA profiling animation above). In this case, we have “frozen” the gel in time to visualize the fragments and compare the samples. The numbers along the left side of the electrophoresis gel table in the Week 5 Assignment Template indicate the number of DNA base pairs in each DNA fragment.
There are eight DNA fragments from each person, representing the paternal chromosomes, light blue and maternal chromosomes, light pink for chromosomes 2, 5, 7, and 13.
Each DNA fragment is labeled as follows:
D 248 BP___TPOX
#2 Pater. Chromo
D 248 BP___TPOX
#2 Mater. Chromo
⦁ the sample letter designation – A, B, C, D, E
⦁ the total number of base pairs in the fragment – 248 BP, etc
⦁ the number of the chromosome – 2, 5, 7, 13
⦁ the FBI designation for the DNA locus – TPOX, etc.
⦁ the color of the fluorescent PCR primer – yellow, red, blue, green
⦁ whether it is paternal or maternal chromosome – light blue or light pink
The electrophoresis gel table, includes only the profiles of Anna Nicole Smith and the two possible fathers (samples A, B, & C). We need to have a sample of the baby girl’s DNA to compare with the DNA samples of the parents.The two tables containing DNA Samples D and E represent the DNA samples of the two actual parents.
Make a Baby
To make a baby, you need to select chromosomes from each parent to represent the genetic make-up of the gametes that, after fertilization, will represent the genetic make-up of the baby. Then, you will take that chromosome information and plot it in the “baby” column or Sample D + E column, of the electrophoresis gel table and compare it with the other DNA samples to determine the two parents.
Here are chromosome-like representations of the DNA data for the actual parents to help you visualize the process of meiosis that will produce the gametes we need to make a baby.
Chromosomes for DNA samples D and E before DNA replication

Meiosis I – Metaphase Sample E

Meiosis I – Later Metaphase (Sample E)

Full Sized Images
Note the random arrangement of these 4 homologous pairs of chromosomes during meiosis. With 4 pairs of homologous chromosomes, this is only one of 16 possible chromosome alignments during meiosis (2 raised to the 4th power).
The gamete for sample D (one parent) should contain one chromosome #2, one #5, one #7 and one #13. Since meiosis produces random arrangements of maternal and paternal homologous chromosomes through independent assortment, you can randomly select either the light blue or light pink chromosome for homologous pairs #2, #5, #7, and #13.
Similarly, select 4 chromosomes for the gamete for sample E (the other parent).
To complete the electrophoresis gel table in your MS Word document, highlight and copy the four chromosomes you have chosen for the gamete from the sample D table and the four you have chosen for the gamete from the sample E table and paste them into the proper location (based on the number of base pairs in the DNA fragment) in the “baby” column of the electrophoresis gel table.
Compare the DNA profile of the baby you created with the DNA profiles of samples, A, B, and C and determine which samples represent the two parents of your baby.

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