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Answer minimum of 250 words. Must use provided material (PDF book) as well as one additional source to help support answer. Please use in-text citations in the beginning of each new paragraph. Reference/cite in APA format. DO NOT PLAGIARIZE. (Please use clear concise sentences without repeating previous statements) Here is the reference for the PDF: Saferstein, Richard (2014) Criminalistics: An Introduction to Forensic Science, 11th edition.1.) Option 4: A woman reports being mugged by a masked assailant, whom she scratched on the arm during a struggle. The victim gives the police a good description of her attacker, but she is not sure whether the assailant was male or female. Describe the steps and procedures you might use to determine the sex of the attacker.
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chapter
15
DNA: the indispensable
forensic science tool
Learning Objectives
L
I
D
D
E
L
L
,
After studying this chapter you should be able to:
Thow they are
t Name the parts of a nucleotide and explain
I
linked together to form DNA
t Understand the concept of base pairing asFit relates to the
double-helix structure of DNA
F
t Contrast DNA strands that code for the production
of proteins
A
with strands that contain repeating base sequences
N
t Explain the technology of polymerase chain
Y reaction (PCR)
and how it applies to forensic DNA typing
t Understand the concept of electrophoresis
1
5
t Describe the difference between nuclear and
6 mitochondrial
DNA
8
t Understand the use of DNA computerizedTdatabases in
criminal investigation
S
t Understand the structure of an STR
ISBN: 978-1-323-16745-8
t List the necessary procedures for the proper preservation
of bloodstained evidence for laboratory DNA analysis
KEY TERMS
amelogenin gene
amino acids
buccal cells
chromosome
complementary base
pairing
deoxyribonucleic acid
(DNA)
electrophoresis
epithelial cells
human genome
hybridization
low copy number
mitochondria
multiplexing
nucleotide
picogram
polymer
polymerase chain
reaction (PCR)
primer
proteins
replication
restriction fragment
length polymorphisms (RFLPs)
sequencing
short tandem repeat
(STR)
substrate control
tandem repeat
touch DNA
Y-STRs
Criminalistics: An Introduction to Forensic Science, Eleventh Edition, by Richard Saferstein. Published by Prentice Hall. Copyright © 2015 by Pearson Education, Inc.
378
CHAPTER 15
deoxyribonucleic acid (DNA)
The molecules carrying the body’s
genetic information; DNA is
double stranded in the shape of a
double helix.
chromosome
A rodlike structure in the cell
nucleus, along which the genes are
located; it is composed of DNA
surrounded by other material,
mainly proteins.
polymer
A substance composed of a large
number of atoms; these atoms are
usually arranged in repeating units,
or monomers.
nucleotide
The unit of DNA consisting of one
of four bases—adenine, guanine,
cytosine, or thymine—attached to
a phosphate–sugar group.
A
What Is DNA?
S
P
G
S
P
T
The discovery of deoxyribonucleic acid (DNA), the deciphering of its structure, and the decoding of its genetic information were turning points in our understanding of the underlying concepts
of inheritance. Now, with incredible speed, as molecular biologists unravel the basic structure of
genes, we can create new products through genetic engineering and develop diagnostic tools and
treatments for genetic disorders.
For a number of years, these developments were of seemingly peripheral interest to forensic
scientists. All that changed when, in 1985, what started out as a more or less routine investigation into the structure of a human gene led to the discovery that portions of the DNA structure
of certain genes are as unique to each individual as fingerprints. Alec Jeffreys and his colleagues
at Leicester University, England, who were responsible for these revelations, named the process
for isolating and reading these DNA markers DNA fingerprinting. As researchers uncovered new
approaches and variations to the original Jeffreys technique, the terms DNA profiling and DNA
typing came to be applied to describe this relatively new technology.
This discovery caught the imagination
of the forensic science community because forensic
L
scientists have long desired to link with certainty biological evidence such as blood, semen, hair,
or tissue to a single individual.IAlthough conventional testing procedures had gone a long way
toward narrowing the source ofD
biological materials, individualization remained an elusive goal.
Now DNA typing has allowed forensic scientists to accomplish this goal. The technique is still
D since its introduction, DNA typing has become routine in
relatively new, but in the few years
public crime laboratories and has
E been made available to interested parties through the services
of a number of skilled private laboratories. In the United States, courts have overwhelmingly
L the reliability of its scientific underpinnings.
admitted DNA evidence and accepted
S
P
L
,
Inside each of 60 trillion cells in the human body are strands of genetic material called
chromosomes. Arranged alongTthe chromosomes, like beads on a thread, are nearly 25,000
genes. The gene is the fundamental
I unit of heredity. It instructs the body cells to make proteins
that determine everything from hair color to our susceptibility to diseases. Each gene is actually
composed of DNA specifically F
designed to carry out a single body function.
Interestingly, although DNA
Fwas first discovered in 1868, scientists were slow to understand
and appreciate its fundamental role in inheritance. Painstakingly, researchers developed evidence
A by which genetic instructions are passed from one generathat DNA was probably the substance
tion to the next. But the major N
breakthrough in comprehending how DNA works did not occur
until the early 1950s, when two researchers, James Watson and Francis Crick, deduced the strucY is an extraordinary molecule skillfully designed to carry out
ture of DNA. It turns out that DNA
the task of controlling the genetic traits of all living cells, plant and animal.
1
Before examining the implications
5 of Watson and Crick’s discovery, let’s see how DNA is constructed. DNA is a polymer. As we will learn in Chapter 12, a polymer is a very large molecule
6
made by linking a series of repeating units.
8
NUCLEOTIDES In the case of DNA, the repeating units are known as nucleotides. A nucleotide
T a phosphorus-containing group, and a nitrogen-containing
is composed of a sugar molecule,
molecule called a base. FigureS
15–1 shows how nucleotides can be strung together to form a
Structure of DNA
C
S
P
DNA strand. In this figure, S designates the sugar component, which is joined with a phosphate
group to form the backbone of the DNA strand. Projecting from the backbone are the bases.
The key to understanding how DNA works is to appreciate the fact that only four types of
bases are associated with DNA: adenine, cytosine, guanine, and thymine. To simplify our discussion of DNA, we will designate each of these bases by the first letter of their names. Hence,
A will stand for adenine, C will stand for cytosine, G will stand for guanine, and T will represent
thymine.
Again, notice in Figure 15–1 how the bases project from the backbone of DNA. Also, although this figure shows a DNA strand of four bases, keep in mind that in theory there is no
limit to the length of the DNA strand; in fact, a DNA strand can be composed of a long chain
with millions of bases. The information just discussed was well known to Watson and Crick by
Criminalistics: An Introduction to Forensic Science, Eleventh Edition, by Richard Saferstein. Published by Prentice Hall. Copyright © 2015 by Pearson Education, Inc.
ISBN: 978-1-323-16745-8
FIGURE 15–1
How nucleotides can be
linked to form a DNA
strand. S designates
the sugar component,
which is joined with
phosphate groups (P) to
form the backbone of
DNA. Projecting from
the backbone are four
bases: A, adenine; G,
guanine; T, thymine;
and C, cytosine.
DNA: THE INDISPENSABLE FORENSIC SCIENCE TOOL
379
the time they set about detailing the structure of DNA. Their efforts led to the discovery that the
DNA molecule is actually composed of two DNA strands coiled into a double helix. This can be
thought of as resembling two wires twisted around each other.
As these researchers manipulated scale models of DNA strands, they realized that the
only way the bases on each strand could be properly aligned with each other in a double-helix
configuration was to place base A opposite T and G opposite C. Watson and Crick had solved
the puzzle of the double helix and presented the world with a simple but elegant picture of DNA
(see Figure 15–2).
COMPLEMENTARY BASE PAIRING The only arrangement possible in the double-helix
configuration was the pairing of bases A to T and G to C, a concept that has become known as
complementary base pairing. Although A–T and G–C pairs are always required, there are no
restrictions on how the bases are to be sequenced on a DNA strand. Thus, one can observe the
sequences T–A–T–T or G–T–A–A or G–T–C–A. When these sequences are joined with their
L
complements in a double-helix configuration, they pair as follows:
T A T T
| |
| |
A T A A
complementary base pairing
The specific pairing of base A
with T and base G with C in
double-stranded DNA.
G IT C A
| D
| | |
C A G T
G T A A
| | | |
C A T T
D
Any base can follow another on a DNA strand, which means that the possible number of difE human chromosome has
ferent sequence combinations is staggering! Consider that the average
DNA containing 100 million base pairs. All of the human chromosomes
taken together contain
L
about 3 billion base pairs. From these numbers, we can begin to appreciate the diversity of DNA
L
,
T
I
F
F
A
N
Y
G
A
S
P
C
S
G
P
S
T
C
T
A
1
5
6
S
P
8
TS P
S S
P
ISBN: 978-1-323-16745-8
P
S
G
C
S
FIGURE 15–2
A representation of a DNA double helix. Notice how bases G and C pair with each
other, as do bases A and T. This is the only arrangement in which two DNA strands can
align with each other in a double-helix configuration.
Criminalistics: An Introduction to Forensic Science, Eleventh Edition, by Richard Saferstein. Published by Prentice Hall. Copyright © 2015 by Pearson Education, Inc.
380
CHAPTER 15
WEBEXTRA 15.1
and hence the diversity of living organisms. DNA is like a book of instructions. The alphabet
used to create the book is simple enough: A, T, G, and C. The order in which these letters are arranged defines the role and function of a DNA molecule.
What Is DNA?
DNA at Work
proteins
Polymers of amino acids that play
basic roles in the structures and
functions of living things.
amino acids
The building blocks of proteins;
there are twenty common amino
acids; amino acids are linked to
form a protein; the types of amino
acids and the order in which they’re
linked determine the character of
each protein.
Normal
hemoglobin
Sickle-cell
hemoglobin
1
valine
valine
2
histidine
histidine
3
leucine
leucine
4
threonine
threonine
5
proline
proline
6
glutamate
valine
7
glutamate
glutamate
(a)
(b)
FIGURE 15–3
(a) A string of amino acids
composes one of the protein chains of hemoglobin.
(b) Substitution of just one
amino acid for another in
the protein chain results in
sickle-cell hemoglobin.
The inheritable traits that are controlled by DNA arise out of its ability to direct the production
of complex molecules called proteins. Proteins are actually made by linking a combination of
amino acids. Although thousands of proteins exist, they can all be derived from a combination
of up to 20 known amino acids. The sequence of amino acids in a protein chain determines the
shape and function of the protein. Let’s look at one example: The protein hemoglobin is found
in our red blood cells. It carries oxygen to our body cells and removes carbon dioxide from these
cells. One of the four amino acid
L chains of “normal” hemoglobin is shown in Figure 15–3(a).
Studies of individuals with sickle-cell anemia show that this inheritable disorder arises from the
I in their red blood cells. An amino acid chain for “abnormal”
presence of “abnormal” hemoglobin
hemoglobin is shown in FigureD15–3(b). Note that the sole difference between “normal” and
“abnormal” or sickle-cell hemoglobin arises from the substitution of one amino acid for another
D
in the protein chain.
The genetic information that
E determines the amino acid sequence for every protein manufactured in the human body is stored in DNA in a genetic code that relies on the sequence of
Lalphabet of DNA is simple—A, T, G, and C—but the key to debases along the DNA strand. The
ciphering the genetic code is to L
know that each amino acid is coded by a sequence of three bases.
Thus, the amino acid alanine is coded by the combination C–G–T; the amino acid aspartate is
, and the amino acid phenylalanine is coded by the combinacoded by the combination C–T–A;
tion A–A–A. With this code in hand, we can now see how the amino acid sequence in a protein
chain is determined by the structure of DNA. Consider the DNA segment
T
I
The triplet code contained within this segment translates into
F
[C–G–T] – [C–T–A] – [A–A–T] – [C–G–T]
F aspartate phenylalanine alanine
alanine
or the protein chain
A
alanine Naspartate
phenylalanine
alanine
Y
Interestingly, this code is not restricted
to humans. Almost all living cells studied to date use the
–C–G–T–C–T–A–A–A–A–C–G–T–
same genetic code as the language of protein synthesis.1
If we look at the difference between “normal” and sickle-cell hemoglobin (see Figure 15–3),
1 by substituting one amino acid (valine) for another (glutawe see that the latter is formed
mate). Within the DNA segment
5 that codes for the production of normal hemoglobin, the letter
sequence is
6–[C–C–T]–[G–A–G]–[G–A–G]–
8 proline glutamate glutamate
Individuals with sickle-cell disease
T carry the sequence
–[C–C–T]–[G–T–G]–[G–A–G]–
S
proline
valine
glutamate
1
Instructions for assembling proteins are actually carried from DNA to another region of the cell by ribonucleic acid
(RNA). RNA is directly involved in the assembly of the protein using the genetic code it received from DNA.
Criminalistics: An Introduction to Forensic Science, Eleventh Edition, by Richard Saferstein. Published by Prentice Hall. Copyright © 2015 by Pearson Education, Inc.
ISBN: 978-1-323-16745-8
Thus, we see that a single base or letter change (T has been substituted for A in valine) is the underlying cause of sickle-cell anemia, demonstrating the delicate chemical balance between health
and disease in the human body.
As scientists unravel the base sequences of DNA, they obtain a greater appreciation for the
roles that proteins play in the chemistry of life. Already the genes responsible for hemophilia,
DNA: THE INDISPENSABLE FORENSIC SCIENCE TOOL
Duchenne muscular dystrophy, and Huntington’s disease have been located. Once scientists have
isolated a disease-causing gene, they can determine the protein that the gene has directed the cell
to manufacture. By studying these proteins—or the absence of them—scientists will be able to
devise a treatment for genetic disorders.
A 13-year project to determine the order of bases on all 23 pairs of human chromosomes
(also called the human genome) is now complete. Knowing where on a specific chromosome
DNA codes for the production of a particular protein is useful for diagnosing and treating genetic
diseases. This information is crucial for understanding the underlying causes of cancer. Also,
comparing the human genome with that of other organisms will help us understand the role and
implications of evolution.
Replication of DNA
L
Once the double-helix structure of DNA was discovered, how DNA duplicated itself before cell
I
division became apparent. The concept of base pairing in DNA suggests
the analogy of positive
and negative photographic film. Each strand of DNA in the double
D helix has the same information; one can make a positive print from a negative or a negative from a positive.
381
human genome
The total DNA content found
within the nucleus of a human cell;
it is composed of approximately
three billion base pairs of genetic
information.
replication
The synthesis of new DNA from
existing DNA.
polymerase chain reaction
(PCR)
A technique for replicating or
copying a portion of a DNA strand
outside a living cell; this technique
leads to millions of copies of the
DNA strand.
D
The Process of Replication
E
The synthesis of new DNA from existing DNA begins with the unwinding
of the DNA strands in
L
the double helix. Each strand is then exposed to a collection of free nucleotides. Letter by letter, the
double helix is re-created as the nucleotides are assembled in the L
proper order, as dictated by the
principle of base pairing (A with T and G with C). The result is the ,emergence of two identical cop-
ISBN: 978-1-323-16745-8
ies of DNA where before there was only one (see Figure 15–4). A cell can now pass on its genetic
identity when it divides.
Many enzymes and proteins are involved in unwinding the T
DNA strands, keeping the two
DNA strands apart, and assembling the new DNA strands. For example, DNA polymerases are
I
enzymes that assemble a new DNA strand in the proper base sequence
determined by the original, or parent, DNA strand. DNA polymerases also “proofread” the
F growing DNA double helices
for mismatched base pairs, which are replaced with correct bases.
F to be of only acaUntil recently, the phenomenon of DNA replication appeared
demic interest to forensic scientists interested in DNA for identification.
However,
A
this changed when researchers perfected the technology of using DNA polymerases
N technique is
to copy a DNA strand located outside a living cell. This laboratory
known as polymerase chain reaction (PCR). Put simply, PCR
Y is a technique
designed to copy or multiply DNA strands in a laboratory test tube.
In PCR, small quantities of DNA or broken pieces of DNA found in crimescene evidence can be copied with the aid of a DNA polymerase.
1 The copying
process is highly temperature dependent and can be accomplished in an automated fashion using a DNA thermal cycler (see Figure 15–5).5Each cycle of
the PCR technique results in a doubling of the DNA, as shown 6
in Figure 15–4.
Within a few hours, 30 cycles can multiply DNA a billionfold. Once DNA copies are
in hand, they can be analyzed by any of the methods of modern8molecular biology. The ability to multiply small bits of DNA opens new and exciting avenues
T for forensic scientists to
explore. It means that sample size is no longer a limitation in characterizing DNA recovered
S
from crime-scene evidence.
Parent DNA
unravels
New double
helices formed
FIGURE 15–4
Replication of DNA. The
strands of the original DNA
molecule are separated,
and two new strands are
assembled.
DNA Typing with Short Tandem Repeats
Tandem Repeats
Geneticists have discovered that portions of the DNA molecule contain sequences of letters that
are repeated numerous times. In fact, more than 30 percent of the human genome is composed of
repeating segments of DNA. These repeating sequences, or tandem repeats, seem to act as filler
or spacers between the coding regions of DNA. Although these repeating segments do not seem
tandem repeat
A region of a chromosome that
contains multiple copies of a core
DNA sequence that are arranged
in a repeating fashion.
Criminalistics: An Introduction to Forensic Science, Eleventh Edition, by Richard Saferstein. Published by Prentice Hall. Copyright © 2015 by Pearson Education, Inc.
382
CHAPTER 15
inside the science
L
I
D
D
E
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L
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Polymerase Chain Reaction
The most important feature of PCR is the knowledge
that an enzyme called DNA polymerase can be directed to synthesize a specific region of DNA. In a
relatively straightforward manner, PCR can be used
to repeatedly duplicate or amplify a strand of DNA
millions of times. As an example, let’s consider a segment of DNA that we want to duplicate by PCR:
–G–T–C–T–C–A–G–C–T–T–C–C–A–G–
–C–A–G–A–G–T–C–G–A–A–G–G–T–C–
To perform PCR on this DNA segment, short sequences of DNA on each side of the region of interest
must be identified. In the example shown here, the
short sequences are designated by boldface letters in
the DNA segment. These short DNA segments must
be available in a pure form known as a primer if the
PCR technique is going to work.
The first step in PCR is to heat the DNA strands to
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