Chapter 12

DNA Analysis

Identify individuals from unique genetic code

In every nucleated cell in the human body

Can be extracted from blood, semen, urine, bone, hair follicles, and saliva

In the nucleus of each cell are

46 chromosomes.

Each chromosome is made of long

strands of DNA wrapped

around proteins called histones.

You have 23 pairs of chromosomesOne copy is from each parent.

A GENE IS A SEGMENT OF DNA THAT CONTAINS THE INSTRUCTION S TO MAKE A

PROTEIN

There are about 20,000-25,000 genes in the human genome. Most of your DNA (98%) does not code for proteins.

DNA structureDeoxyribonucleic Acid is a macromolecule containing the sugar deoxyribose.

It is a polymer made of two strands of repeating units called nucleotides.

Each nucleotide is made of three parts…a sugar, a phosphate group, and a nitrogenous base.

There are only four different nitrogenous bases… Adenine

ThymineCytosineGuanine

Eye color

Hair color

Skin color

freckles

Widows peak

Gene; a segment of DNA that codes for a particular protein

One strand of

nucleotides

The hydrogen bonds are very weak, so the two strands can “unzip” allowing the base sequence to be “read” when the DNA copies itself, or when the gene’s instructions are used to create proteins.

Every three bases codes

for one amino acid. A long

string of amino acids make up a

protein, and our proteins

that we make give us our

traits.

The order of the 3 billion base pairs is 99.9% identical in all humans. The unique 0.1% gives us incredible diversity.

EinsteinMozart

Jack the Ripper

YOU!

Types of DNA

Nuclear found in the nucleus constitutes 23 pairs

of chromosomes inherited from both parents

each cell contains only one nuclei

Mitochondrial found in the

cytoplasm is inherited only

from mother each cell contains

hundreds to thousands of mitochondria

can be found in skeletal remains

Nuclear DNA is present in the head of the sperm. Mitochondrial DNA is present in the tail. At conception, the head of the sperm enters the egg and unites with the nucleus. The tail falls off, losing the father’s mitochondrial DNA.

Typically blood and other bodily fluids provide DNA for forensic testing and determining a DNA

profile, or fingerprint.

USES OF DNA FINGERPRINTING:

1. IDENTIFY POTENTIAL SUSPECTS2. CLEAR THE WRONGLY ACCUSED

3. IDENTIFY CRIME AND CATASTROPHE VICTIMS4. ESTABLISH PATERNITY

5. MATCH ORGAN DONORS AND RECIPIENTS

RFLP Analysis

Restriction FragmentLength Polymorphism

1. After isolating the DNA from the cell, restriction enzymes are used to “chop up” the DNA into small pieces (or DNA “fragments”). Different restriction enzymes recognize different DNA sequences and therefore cut the DNA at different places in the sequence. You end up with many fragments of different lengths (they’re polymorphic).

Animation

2. Now, the many fragments are separated by gel electrophoresis. A gel provides a barrier through which the DNA fragments can slowly travel. An electrical current draws the negatively charged DNA from one end of the gel to the other, but the polymorphic fragments don’t travel at the same speed, so they’re separated by size and charge.

AnimationVirtual lab

Unique banding pattern is your DNA profile or DNA fingerprint

Polymerase Chain Reaction (PCR)

• Make millions of copies of DNA from a small sample

• Quick and easy in the lab, DNA less susceptible to degradation

• Requires 50x less DNA than what is needed for RFLP

• Contaminant DNA will be amplified as well

Short Tandem Repeats (STR)

Used more commonly than RFLP because:

• Takes less time

• Requires less of a sample size

• Is more exclusionary (eliminates more people as the source of the DNA)

STR’s are locations (loci) on the chromosome that contain short sequences

of 2 to 5 bases that repeat themselves in the DNA molecule. They are “markers” not found in the “coding” part of a gene.

THO1 One commonly used STR 5 – 11 repeats of A-A-T-G on chromosome 11 in

the introns of the tyrosine hydroxylase gene

There are 7 variants of THO1 in humans

Short Tandem Repeats (STR)STR typing is visualized by peaks shown on a graph.

Each peak represents the size of the DNA fragment.

FBI’s CODIS DNA Database

Combined DNA Index System Used for linking serial crimes and

unsolved cases with repeat offenders

Launched October 1998 Links all 50 states Requires >4 RFLP markers and/or

13 core STR markers

CODIS

CODIS

1. Probability of Identity

Is a measure of the likelihood that 2 random

individuals will have an

identical STR type

2. Probability is determined

By multiplying their frequencies

3. Probability ofanother unrelated individual

Having the first 3 STRs match is

1 in 5000 STR African-American U.S

Caucasian D3S1358 0.097 0.080 vWA 0.074 0.068 FGA 0.036 0.041

8/100 x 6.8/100 x 4.1/100 = 223 / 1 000 000

≈ 1 / 5000 in the U.S. Caucasian population

4. The probability of frequency

For the first 6 STRs

is 1 in 2 million

5. The probability of frequency of

all 13 STRs is

1 in trillions (1 trillion= 1 000 000 000

000)

World population is over 7 billion!

Three Possible Outcomes

Match—The DNA profile appears the same. Lab will determine the frequency.

Exclusion—The genotype comparison shows profile differences that can only be explained by the two samples originating from different sources.

Inconclusive—The data does not support a conclusion as to whether the profiles match.

DNA Interactive

The website below has a STR animation demonstration. Click on human identification, profiling and then on the third circle called Today’s DNA Profiling to see the demonstration.

http://www.dnai.org/d/index.html

Nicole Brown Simpson’s blood a match for the blood on a piece of evidence.

Data

Uses of DNA Fingerprinting

A. Identification of remains

Case Study:

The Angel of Death:

Josef Mengele

Josef Mengele was a Nazi war criminal

notorious for grotesque human experiments that he carried out at the Auschwitz concentration camp.

After the Second World War he fled from the Allies and escaped to South America.

The fugitive succeeded in living out the rest of his days without being caught.

Embu1985

WolfgangGerhardDied 1979

Using DNA extracted from blood provided by Mengele’s ex-wife and son, it was concluded that it was more than 99.94% certain that the skeleton was Mengele’s

Irene

Rolf

B. Paternity Cases

Who’s your daddy?

1.

2.

1. 2.

Case Study:

The Sally Hemings

and

Thomas

Jefferson

Controversy

Thomas Jefferson (April 13, 1743–July 4, 1826)

Third president of the United States (1801–1809)

Principal author

of the Declaration of Independence and one of the most influential Founding Fathers for his promotion of the ideals of republicanism in the United States

WhenPresident John F. Kennedy welcomed forty-nine Nobel Prize winners to the White House in 1962 he said, "I think this is the most extraordinary collection of talent and of human knowledge that has ever been gathered togetherat the White House– with the possible exceptionof when Thomas Jefferson dined alone.”

Jefferson has been consistently ranked by scholars as one of the GREATEST

U.S.PRESIDENTS.

Thomas Jefferson – an enigma

Jefferson owned

many slaves over

his lifetime.

Some find it baffling

that Thomas Jefferson

owned slaves yet was

outspoken in saying that slavery was

immoral

and it should be abolished.

Biographers point out thatJefferson was deeply in debtand had encumbered his slaves by notes

and

mortgages; he chose

not to free them until he finally was debt-free,

which he never was.

Elizabeth Hemings John Wayles

John’s slave Jefferson’s Father-in-law

Sally Hemings (1773)

1776

3a.

1802..James T.Callender(a disappointed office-seeker)

Jefferson had “kept as

his concubine, one of his own slaves”

and had“several children”

by her

In a Richmond newspaper

Two of Sally’s children:

Madison and Eston claimed that

Jefferson was their father. This belief was passed down

through the generations.

The Jefferson-Hemings storyDenied by his children on practical and moral grounds

Jefferson descendants claim that Jefferson’s nephews – Peter and Samuel Carr – were the fathers of the light-skinned Monticello slaves some thought to be Jefferson’s children.

The Jefferson–Hemings Story

was sustained throughout the 19th century by:

abolitionistsBritish critics of US democracy

THE DNA TESTS

Conducted by Dr. Eugene Foster and a team of geneticists in 1998

No direct male descendants of Thomas Jefferson have survived

The DNA Study

Tested Y- chromosomal DNA samples from male-line descendants of Field Jefferson (Thomas Jefferson’s

uncle), John Carr (paternal grandfather of

Samuel and Peter Carr) Eston Hemings (Sally’s second son) Thomas C. Woodson (reputed to be

Sally’s first son)

The DNA Study:

(1) Found NO LINK between the descendants of Field Jefferson and Thomas C. Woodson (reputed to be Sally’s first son, but no records of his birth have been found to substantiate this)

X

(2) Found NO LINK between Hemings and Carr descendants

X

(3) Found that an individual

carrying the male Jefferson Y- chromosome fathered Eston Hemings (born 1808), the last known child of Sally

Hemings.

Does this mean that Thomas Jefferson was definitely the father of Eston Hemings?

No, it means that he COULD BE the father of Eston Hemings.

There were 25 adult male Jeffersons

who carried this chromosome living in Virginia at the time, and a few of them are known to have visited Monticello

November, 1998

“Jefferson Fathered Slave’s Last Child”

The Thomas Jefferson Memorial Foundation issued a report

in January 2000 concluding that there is a strong likelihood that Thomas Jefferson was the father of at least one and perhaps all the children of Sally Hemings.

May 27, 2002

The Monticello Association

An organization for descendants

of Thomas Jefferson refused to recognize and

admit any descendants of Sally

Hemings

The Monticello Association, decided to continue to restrict membership to Jefferson's descendants through his daughters Martha and Maria.

Many elements of the Jefferson- Hemings story are widely accepted :

Sally Hemings (1773-1835) was a slave at

Monticello, She lived in Paris

with Jefferson and two of his daughters from 1787-1789

Sally had 6 children

The births of Sally’s children were recorded in Monticello records:

Harriet (born 1795; died in infancy) Beverly (born 1798) An unnamed daughter (born 1799;

died in infancy) Harriet (born 1801) Madison (born 1805) Eston (born 1808)

Sally Hemings:

Nursemaid - companionto Jefferson’s daughter

Maria

Lady’s maid to daughters Martha and Maria

seamstress

No known images of Sally Hemings

?

Sally left no known written accounts

It is not known if she was

literate

There are only a few..

Scattered references to Sally in Thomas Jefferson’s records

There is nothing to distinguish her from any other members of her family or any other slaves

Records indicate that..

At the likely conception timesof Sally’s six known children

Sally’s children were..

Light-skinned and three of them, daughter Harriet and sons Beverly and Eston lived as members of white society

According to contemporary accounts

Some of Sally’s children

Strongly resembled Jefferson

Freed by Jefferson during his lifetime: Robert Hemings (1762-1819), freed 1794 James Hemings (1765-1801), freed 1796

Freed in 1826-1827, by the terms of Jefferson's will:

Joseph (Joe) Fossett (1780-1858) Burwell Colbert (1783-1850+) Madison Hemings (1805-1856) John Hemmings (1776-1833) Eston Hemings (1808-1856)

Left Monticello, with Jefferson's tacit consent, in 1804 and 1822:

James Hemings (born 1787) Beverly Hemings (born 1798) Harriet Hemings (born 1801)

JEFFERSON GAVE FREEDOM TO

NO OTHER NUCLEAR

SLAVE FAMILY

Jefferson did not free Sally Hemings. She was permitted to leave Monticello by Maria Jefferson Randolph not long after Jefferson’s death in 1826 and went to live with her sons Madison and Eston in Charlottesville.

Eston Hemings Changed his name to Eston Hemings Jefferson in 1852

Madison Hemings stated in 1873 that he and his siblings were Thomas Jefferson’s children.

The descendants of Eston Hemings

Who livedas whites,passeddown

A family history of being related to Thomas Jefferson

The descendants ofMadison Hemings

Who have lived as African-Americans

have passed a family

history of descent from Thomas

Jefferson and

Sally Hemings

The Thomas Jefferson Foundation

Stands by its original findings - that the weight of evidence suggests that Jefferson probably was the father of Eston Hemings and perhaps the father of all of Sally Heming’s children – but is ready to review new evidence at any time and to reassess its understanding of this matter in the light of new information.