1. Chapter 10 Advanced Concepts in DNA
© 2012 Cengage Learning. All Rights Reserved

2. Introduction—Objectives
Discuss the structure and function of DNA.
Explain what causes variation in DNA.
Differentiate between the various types of DNA analysis.
Compare and contrast the methods of extracting DNA.
Explain the proper methods of collecting DNA evidence at a crime scene.
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

3. Introduction—Vocabulary
DNA extraction—process of removing DNA from a cell; procedures include Chelex extraction, organic extraction, and differential extraction
homologous chromosomes—pair of chromosomes in which one chromosome was inherited from the male parent and the other was inherited from the female parent
Nucleotide—subunit of DNA and other nucleic acids; made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

4. Introduction—Vocabulary
polymerase chain reaction (PCR)—technique used to make billions of copies of a specific segment of DNA; allows very minute samples of DNA to be copied billions of times
primer—small piece of DNA used to begin and end replication during PCR
short tandem repeat (STR)—short segment of DNA in which the same sequence of two to six base pairs is repeated many times; varying numbers of repeats found among individuals
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

5. A 200-Year Old Mystery
August 13, 1792, the French royal family is arrested and imprisoned.
The king and queen were executed.
The heir lived two more years.
Did he die in prison or escape?
DNA samples from the remains of the king, queen and suspected dauphin were compared. 5
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

6. Introduction
Deoxyribonucleic acid (DNA)—the genetic material that makes each individual unique.
Only identical twins have the same DNA
DNA copies itself when cells divide
DNA contains the blueprint for making proteins essential for life processes
DNA is found in biological evidence
DNA is individual evidence
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

7. Structure and Function (Obj 10.2)
Nucleotides—subunits of DNA
Deoxyribose
Phosphate group
Nitrogenous base
Adenine
Thymine
Cytosine
Guanine
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

8. Structure and Function (Obj 10.2)
Each nitrogenous base can form hydrogen bonds with a specific base on a complementary strand of DNA
Adenine always pairs with thymine
Guanine always pairs with cytosine
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

9. Structure and Function (Obj 10.2)
Nitrogenous base pairs form the rungs of a twisted ladder and carry a lot of information
Sugar and phosphate groups form the edges of the ladder
Genes—sections of DNA that code for a protein
Proteins catalyze, regulate, and control chemical reactions in the cell.
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

10. Structure and Function (Obj 10.2)
Alleles—an alternative form of a gene for a certain trait.
An individual inherits two alleles for each gene, one from each parent.
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

11. Structure and Function (Obj 10.2)11
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

12. What Causes Variation in DNA? (Obj 10.2)
99.5% of DNA is the same for everyone
0.5% of DNA is what makes us unique
Homozygous—when two alleles are identical for a particular trait
Heterozygous—when two alleles are different
Marker—a sequence of DNA base pairs associated with a specific trait
Matching markers from two samples determines the likelihood of an individual being the same as the reference sample
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

13. DNA Analysis Procedures (Obj 10.3, 10.4)
Method of extraction varies depending upon
The type of biological evidence analyzed
The amount of evidence available
The type of cells present
Chelex Extraction
Used when a small amount of biological evidence is available
Sample placed in boiling water with Chelex beads
The cells in the sample burst open to expose and preserve DNA
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

14. DNA Analysis Procedures (Obj 10.3, 10.4)
Organic Extraction—removing biological evidence from materials (e.g., blood from bed sheets)
Differential Extraction—separates vaginal epithelial cells from sperm cells with a mild solution of phenol and chloroform
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

15. Measuring Quality and Quantity of DNA (Obj 10.3)
High molecular weight (HMW)—sample contains DNA in large chunks
Restriction fragment length polymorphism (RFLP)—DNA analysis requiring HMW
Polymerase chain reaction (PCR)—analysis used when only small amounts of DNA are available, amplification process
Variable Number of Tandem Repeats (VNTR) —repeating sections of DNA
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

16. DNA Fingerprinting Fingerprinting has several steps
Isolate and purify DNA
Restriction enzymes indicate where DNA can be cut into fragments (the RFLPs)
Gel electrophoresis sorts DNA bands by size
Southern blotting process transfers DNA bands from the gel to a nylon sheet
Population genetics determines probability of another individual having the same profile
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

17. DNA Fingerprinting
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

18. PCR Polymerase Chain Reaction
An enzyme separates a region of DNA and then copies it billions of times
Samples are heated and cooled in a three-step cycle
Denaturing—(heating) separating the two DNA strands
Primer annealing—(cooling) adding primers (markers) to the beginning and ends of targeted sequences
Polymerization—(heating) an enzyme copies the DNA between the two primers
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

19. PCR 19 Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

20. PCR Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

21. STR
Short Tendem Repeats—a short segment of DNA in which the same sequence of 2 to 6 base pairs is repeated many times
Easier and quicker to replicate
Repeating STR patterns are highly variable between individuals; therefore
Matching multiple STRs between individuals has a very low probability
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

22. CODIS Combined DNA Index System An FBI nationwide database
Stores DNA fingerprints of individuals who have been convicted of certain crimes
Open to forensic scientists to compare DNA fingerprints of suspects based on 13 core STR locations
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

23. CODIS Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

24. Collecting DNA Evidence (Obj 10.5)
Biological samples
Avoid contamination
Retain original surface when possible
Reference samples for comparative analysis
Stop degradation
Protect sample from environmental exposure
Remove moisture by drying out and freezing the sample
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

25. Collecting Biological Evidence
Examples
Skin cells
Blood
Saliva
Semen
Hair
Other possibilites?
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

26. Collecting Biological Evidence
Guidelines
Never use bare hands
Avoid sneezing and coughing
Use clean protective gloves for each item collected
Package each sample separately
Air dry evidence located on objects; store in an envelope or paper bag, not plastic bags
Establish a chain of custody
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

27. Collecting Reference Samples
Known samples taken from suspects and victims
Reference samples are compared to evidence collected from the crime scene
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

28. Testing for Blood, Semen, & Saliva
Presumptive tests used at the crime scene
Luminol is the most common method used to detect blood
Sprayed on objects to find bloodstains
Detects blood even when diluted
Chemicals and fluorescent dyes are used to visualize seminal fluid
For saliva, the Phadebas test or starch iodine test detects the presence of amylase
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

29. Mitochondrial DNA (mtDNA) Analysis
mtDNA is inherited from the mother
Easier to extract than nuclear DNA
Less likely to degrade
Each cell has hundreds of copies of mtDNA
Typically extracted from teeth, hair, bones
Take care to avoid altering this evidence for other analyses
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

30. Y-Chromosome Analysis
Passed down through paternal lineage
Beneficial for these situations
Sexual assault
Missing person
Genealogy
Does not provide individual evidence
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

31. Chapter Summary
The discovery of DNA’s existence, structure, and function dates back to the 1800s.
DNA, shaped like a double helix, is made up of a sugar and phosphate backbone with nucleotides on the inside.
The four nitrogenous bases are adenine, guanine, cytosine, and thymine.
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

32. Chapter Summary
The genetic code is nearly universal. The code is always read three bases at a time and codes for amino acids, which combine to form proteins.
DNA isolation and extraction from biological evidence such as blood, semen, and saliva must be done prior to completing a DNA profile. 32
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

33. Chapter Summary
Polymerase chain reaction (PCR) is used to collect and analyze very minute and degraded samples.
Short tandem repeats (STR) are very short segments of DNA in which the same sequence of two to six base pairs is repeated several times.
The STR pattern, being highly variable from person to person, provides matches with higher degrees of certainty.
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

34. Chapter Summary
Once DNA is exposed to an environment outside the body, the DNA begins to degrade, which affects the ability to retrieve a useful result.
When collecting DNA evidence, extra precautions must be taken to ensure it is kept in the best possible condition.
Presumptive tests exist for the three most common types of body fluids found at a crime scene: blood, semen, and saliva.
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved

35. Chapter Summary Mitochondrial DNA is inherited from the mother.
A Y chromosome is inherited by males from their father. Y-chromosome analysis is beneficial in cases involving sexual assault, missing persons, and genealogy.
Most sexual assaults involve a male as the perpetrator. DNA tests that specifically test the genetic content on the Y chromosome can be forensically valuable.
Forensic Science II: Advanced Concepts in DNA, Chapter 10
© 2012 Cengage Learning. All Rights Reserved