Chapter 16 DNA: The Indispensable Forensic Science Tool

DNA

deoxyribonucleic acid

Polymer

molecule made up of repeating simpler units

Double helix

shape of 2 strands of DNA intertwined

Poles of ladder

alternating sugar molecules (deoxyribose) and phosphates

Rungs

nucleotides or bases

• A: Adenine

• G: Guanine

• T: Thymine

• C: Cytosine

Adenine

A Rung

Guanine

G Rung

Thymine

T Rung

Cytosine

C Rung

• Nuclear

• Mitochondrial

A human cell contains two types of DNA:

Nuclear DNA

________ is a very large molecule made by linking a series of repeating units called nucleotides.

• A sugar

• A phosphorous-containing group

• A nitrogen-containing molecule called a base

A nucleotide is composed of:

adenine (A), guanine (G), cytosine (C), and thymine (T).

Four types of bases are associated with the DNA structure:

backbone of DNA.

S designates the sugar component, which is joined with phosphate groups (P) to form the…

The four bases

What projects from the backbone of DNA?

• C-G

• A-T

Specific base pairing between nucleotides in double stranded DNA

Hydrogen bonds

How are the specific base pairings between nucleotides in double stranded DNA held together?

only

Notice how bases G and C pair with each other, as do bases A and T. This is the ________ arrangement in which two DNA strands can align with each other in a double-helix configuration

proteins

DNA directs the production of ________, which are made by combining amino acids.

shape and function of the protein.

The sequence of amino acids in a protein chain determines the…

a particular amino acid.

Each group of three nucleotides in a DNA sequence codes for…

the amino acid glutamine.

What does the G-A-G group of nucleotides code for?

the amino acid alanine.

What does the C-G-T group of nucleotides code for?

Codon

three nucleotide sequence that specifies a specific amino acid

Amino Acids

one of the 20 building blocks of proteins

Proteins

polymers of amino acids that play basic roles in the structures and functions of living things

not function correctly and this is the basis for many diseases and health issues.

If a nucleotide is "changed," for example, a T is substituted for A and G-A-G becomes G-T-G, the "wrong" amino acid is placed in the protein. As a result, the protein may…

hemoglobin

A string of amino acids composes one of the protein chains of ________.

sickle-cell

Substitution of just one amino acid for another in the protein chain of hemoglobin results in ________ hemoglobin.

3 billion

How many bases of DNA are there?

99.9%

How identical is the structure of DNA between people?

25,000-30,000

How many different genes are there?

3%

What percent of the human genome makes proteins?

50%

What percent of the human genome is repetitive sequences?

STR

short tandem repeats is used for individualizing a DNA sample

CODIS (Combined DNA Index System)

is a computer software program developed by the FBI that maintains local, state, and national databases of DNA profiles from convicted offenders, unsolved crime scene evidence, and profiles of missing persons.

• Started being used in 1990

20

Currently, U.S. crime laboratories have standardized on ________ STRs for entry into a national database (CODIS).

CODIS

Allows the comparison of DNA types recovered from crime scene evidence to those of convicted sex offenders and other convicted criminals.

DNA polymerase

enzyme that makes a copy of a specific region of DNA

Primer

short strand of DNA used to target a region of DNA for replication by PCR

Polymerase Chain Reaction

Three steps, repeated 25-40 times: Denaturation, Annealing, Extension

Denaturation

DNA heated to 940C to separate double strands into single strands

Annealing

lower temp to ~ 600C to allow primers to hybridize to complementary sequences in single stranded DNA

Extension

heat to 720C to allow DNA polymerase to add nucleotides one by one to primer in sequence complementary to DNA being copied

Semi-conservative

each new double helix contains one new strand and one old strand and is the exact copy of the template double helix

DNA helicase

enzyme that unwinds the double helix

DNA polymerase

enzyme that matches free nucleotides by complementary base pairing to template strand

and two new strands are assembled.

The strands of the original DNA molecule are separated…

an existing strand of DNA

Synthesis of a new strand of DNA is from…

cell division.

DNA duplicates itself prior to…

unwinding of the DNA strands of the double helix.

DNA replication begins with the…

recreate the double helix, letter by letter, using complementary base pairing.

Each DNA strand is exposed to a collection of free nucleotides that will be used to…

DNA polymerases

Many enzymes and proteins, such as ________, are involved in unwinding the DNA, keeping the DNA strands apart, and assembling the new DNA strands in the proper order.

Polymerase chain reaction (PCR)

________ is a technique for replicating small quantities of DNA or broken pieces of DNA found at a crime scene, outside a living cell.

an understanding of how DNA strands naturally replicate within a cell.

PCR is the product of knowledge gained from…

millions

For the forensic scientist, PCR offers a distinct advantage in that it can amplify small quantities of DNA many ________ of times.

the DNA is heated to separate it into two strands.

What is first in PCR testing?

primers (short strands of DNA used to target specific regions of DNA for replication) are added, which bind with the separated strands.

What is second in PCR testing?

DNA polymerase and free nucleotides (A, T, G, and C) are added to rebuild each of the separated strands.

What is third in PCR testing

25 to 30 times.

How many time is the cycle of PCR testing repeated?

be multiplied a billionfold.

Within a few hours of PCR testing, a short strand of DNA can…

tandem repeats

Portions of the DNA molecule contain sequences of bases that are repeated numerous times, known as ________.

how the ATGCs repeat themselves.

How is one tandem repeat distinguished from another?

filler or spacers

Tandem repeats seem to act as ________ between the coding regions of DNA.

number of repeats

For a particular tandem repeat, there is tremendous variation in the ________ each of us have for that tandem.

Offer a means of distinguishing one individual from another through DNA typing.

Why is it significant that there is tremendous variation in the number of repeats each of us has for that tandem?

STRs

loci on chromosomes that contain polymorphic segments of short tandem repeats of a three to seven base pair core sequence

DNA fingerprint

Extract DNA, run PCR with primers for each STR, separate DNA based on size with gel electrophoresis to get ________.

Restriction Fragment Length Polymorphisms (RFLP)

are length differences associated with relatively long repeating DNA strands and form the basis for one of the first DNA typing procedures.

Disadvantages include being time consuming, labor intensive, not automated, requires large pieces of DNA in large amounts.

What are the disadvantages of RFLPs?

3 to 7 bases in length

STRs normally consist of repeating sequences of ________, and the entire strand of an STR is also very short, less than 450 bases in length.

degradation

STRs are much less susceptible to ________ and may often be recovered from bodies or stains that have been subjected to extreme decomposition.

shortness

STRs are ideal candidates for multiplication by PCR because of their ________, thus overcoming the limited-sample-size problem often associated with crime-scene evidence.

two-band

STRs usually produce a ________ pattern, thus interpretation of mixtures is simplified.

four

An STR pattern arising from two individuals will have up to ________ peaks at one location.

7

How many TH01 variants have been identified in the human genome?

5 to 11 repeats of A-A-T-G

What do TH01 variants contain?

the number of A-A-T-G repeats in the STR.

By examining the distance/speed the STR has migrated during electrophoresis, one can determine…

2

Typically, every person has ________ STR types for TH01, one inherited from each parent.

3.5%

The DNA type known as TH01 6,8 is found in approximately ________ of the population.

hundreds

What makes STRs so attractive to forensic scientists is that ________ of different types of STRs are found in human genes.

smaller

The more STRs one can characterize, the ________ the percentage of the population from which a particular combination of STRs can emanate.

extract and amplify

Using the technology of PCR, one can simultaneously ________ a combination of different STRs.

individualized

any DNA type whose odds of a chance occurrence exceed 1000 times the US population (1 in 260 billion)

Multiplexing

detecting more than one DNA locus in a single analysis

CODIS

Federally maintained database of DNA obtained from crime scenes, convicted violent offenders and missing persons

• Local, state, national levels

States

________ control legislation of DNA samples admissible

• Arrestees: NJ, MD

• No arrestees: PA, DE, NY

17

As of February 2024, CODIS holds over ________ million samples from offenders, 5.3 million from arrestees and 1.3 million from unsolved crimes

350,000 cases

The estimated DNA backlog is ~

• Remains untested for 30 days after being submitted

• Each lab takes in ~4000 cases a month and can process ~2000

25%

________of DNA analyzed by FBI since 1989 has excluded suspects

Amelogenin gene

gene for tooth pulp located on both the X and Y chromosomes

6

The amelogenin gene is ________ bases shorter on X chromosome than on Y chromosome

Males

________, who have an X and a Y chromosome, show two bands of the amelogenin gene.

Females

________, who have two X chromosomes, have just one band of the amelogenin gene.

Y-STRs

short tandem repeats on the Y chromosome

Y

________ chromosome is passed on from father to son

• Useful for paternity suits

• Will not detect female samples

• Only detects one chromosome

• Used when multiple males involved

• Useful when there is a very small quantity of male DNA in a sample with a large amount of female DNA.

Why are detecting Y-STR’s simpler for mixed samples?

in mitochondria in the cytoplasm of cell

Where is Mitochondrial DNA found?

Cannot distinguish between individuals from same maternal line

Why is it significant that mitochondrial DNA is maternally inherited?

copies

Hundreds to thousands of ________ of mtDNA in each cell

• More sensitive than nuclear DNA

• Less prone to degradation