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DNA Science
MU Plant Genome Research
Experience for Teachers
Workshop
Friedrich Miescher
First to extract DNA from nuclei (1869).
 First to ID DNA as a distinct molecule.
 Source of DNA was white blood cells
(WBC).
 WBCs are commonly found in infected
wounds.

Friedrich Miescher (cont.)
Called the substance he isolated nuclein.
 It was high in phosphorus.
 Thought main function was to store
phosphorus.

The Transforming Principle

Avery, Macleod, and McCarty (1943)
discovered different strains of bacteria had
different effects on a mouse.
Transforming Principle (cont.)




What was the transforming principle from the
dead virulent strain that made the avirulent
strain lethal?
Separate the dead virulent strain into fractions
and coinject with avirulent strain.
The DNA fraction contained the transforming
principle.
Controversial result because at that time most
scientists thought proteins were the hereditary
material.
Chargaff Principle

In 1950 found that whatever tissue he took
DNA from the percentage of each
nucleotide was the same. (%G = %C, %A = %T)
Add Some Herstory to History!
Early 1950’s:
Rosalind Franklin, John Randall & Maurice Wilkins
(King's College, London) made beautiful X-ray
diffraction pictures of DNA fibers.
Rosalind Franklin showed her DNA x-ray diffraction
pictures to Watson and Crick.
X-rays
diffract
X-ray
source
X-rays diffract
“Mad Hatters Who Bubble Over About Their New Structure”
Taken from G. Pomerat’s
Diary (Apr 1953):
DNA
Double
Helix,
W&C
Nature
1953
“… Watson and Crick ….have
got the structure of nucleic
acid from a crystallographic
rather than a chemical
standpoint. Their clue came
out of the beautiful x-ray
diagrams produced in
Randall’s lab… They are just
putting the finishing touches
on a huge model about six
feet tall which shows that the
molecule is made up of two
helical chains…”
R. Franklin’s
X-ray Picture
http://vector.cshl.org/resources/pomerat.html
Remembering Rosalind:
British Award Honors Rosalind Franklin
Watson and Crick publish Nature paper
reporting DNA double helix (based in
part on Rosalind’s DNA pictures) in 1953.
Watson, Crick and Wilkins were awarded
1962 Nobel Prize for DNA double-helix.
Rosalind Franklin was not awarded the Nobel Prize,
she died in 1958 (37 years old) of ovarian cancer.
The Franklin Medal now honors Rosalind’s critical
role in the discovery of DNA double helix.
2003: 50 Year Anniversary
of the Discovery of The DNA Double Helix
The famous DNA Double Helix paper
was published in Nature in 1953!
The Double Helix
Two strands of DNA run in opposite
directions, complementing each other and
pairing with hydrogen bonds.
 A and T pair together and C and G pair
together.
 Helix is most often right-handed (B-form).

What Is DNA?
DNA is a chemical contained in every cell of your body.
DNA is a Chemical!?
Yes!
What other kinds of chemicals are in your body?
•We are made up of chemicals, formed from the elements carbon
(C), hydrogen (H), oxygen (O), phosphate (P) and others
•DNA is made up of carbon (C), hydrogen (H), oxygen (O),
phosphate (P)
•We breathe air which contains oxygen molecules (O2).
•We eat food which is composed of chemicals called proteins,
sugars, and fats.
•Our bones are made up largely of calcium (Ca)
•Our bodies make energy by breaking down chemicals such as
sugar!
•We store energy in our body in the form of carbohydrate
chemicals.
DNA
Hereditary material.
 Contains all information to make proteins.
 Linear polymer of nucleotide.
 Each one has sugar, phosphate and a
base.

DNA
Base connected to sugar by β-glucosyl
linkage.
 Nucleotides are connected to one another
by a phosphodiester bond.
 Bases are perpendicular to helix.

Four Bases
A=Adenine
 T=Thymine
 C=Cytosine
 G=Guanine

What Does DNA Look Like?
3D DNA Helix Molecule
•The spheres represent the actual positions
of atoms in the DNA molecule.
•All the atoms together make up the entire
DNA molecule.
•DNA molecule contains 2 DNA polymers
twisted around each other to make the
DNA helix
DNA HELIX
(Tutorial)
3D DNA Double Helix: Two Long DNA Strands
DNA Double Helix:
Two DNA Strands Twisted Around Each Other
“Green”
DNA Strand
“Red”
DNA Strand
3D DNA Strands: Backbone
DNA Strands:
Each DNA Strand Contains One Backbone and Building Block Bases
DNA Backbones are Shown in Dark Green and Dark Red
3D DNA Strands:
Building Blocks are DNA Letters
Each DNA Strand Contains One Backbone and
Many Building Block DNA Letters (Bases)
“Green”
DNA Strand
DNA Letters:
A, G, C, T
“Red”
DNA Strand
How Does DNA Carry Information?
To answer this question we must take a closer look at
DNA.
DNA is a biopolymer
•Polymers are molecules made of repeating units or
building blocks
•DNA has four chemical building blocks symbolized
by the letters A,G,C,& T
•The letters of your DNA are in a specific order that
carries information about you!!
So, a DNA polymer can be represented as a string of
letters:
AG C T TAG G G TAAAC C CATATA
DNA Carries Information in the Sequence of DNA Letters
. . .A G C T T A G G G T A A A C C C A T A G . . .
A gene
• A gene is a length of DNA letters that contain
an instruction for a cell to follow.
• The cell uses specially designed protein machines
to read the information in genes.
The Order of DNA Letters Encodes the Genetic Information
The order or sequence of the A, G, C and T letters in the DNA
polymer encodes the actual genetic information
Example of the DNA letters in a gene:
AGCTTAGGGTAAACCATATAGGGCCATACCCTATCGGTAAGCTT
The specific order of the DNA letters carries
the information.
• Changing the order of the DNA letters will
change the information carried by the gene.
• We will talk about how this happens later!
AGCTTAGGGAAAACCCATATAGGGCCATACCCTATCGGTAAG
Secret of DNA Fingerprinting Lies in the Ability to Detect
Small Differences in DNA Letters Among Individual Samples
Look around the room and see how different we all
look. Then compare any two human genomes:
•The DNA letters are almost the identical order
(sequence) between any two human genomes!
•A very small number (0.1%) of the DNA letters differ
between any two human genomes.
•Two plants that look very
similar may be close or
distantly related because
humans select for desirable
traits in new varieties.
Genes Can Have Hundreds to Millions of DNA Letters
. . .A G C T T A G G G T A A A C C C A T A G . . .
A gene
It can take hundreds, thousands or even a million or
more letters (bases) to “spell out” the instructions in a
single gene.
…and what for?
Controlling Gene Expression
The specific order of DNA bases in a gene encode
a protein product.
Genes have START and STOP signals that specify
the length of the protein chain.
Control DNA region is in front of the “coding region”
and controls expression of the gene.
GENE
Control DNA region is
called a promoter.
+1
PROMOTER
mRNA
DNA region carrying
protein information is
called the coding region.
PROTEIN CODING REGION
Genes Contain Instructions for Building Proteins
Genes contain instructions for making proteins, one of the major types
of the molecules of life, or “biomolecules”
Proteins, like DNA, are polymers
•
Protein building blocks are called amino acids
•
Amino acids are strung together into long, linear polymers by
following the instructions in genes
•
In general, a gene encodes the instructions for one protein
When a gene is “misspelled,” the protein made from it
•
may be made with an incorrect amino acid
•
may not work properly
Review of Gene Expression Pathway in Cells
GENE DNA
mRNA copy of gene
mRNA goes to cytoplasm
Focus on the Genetic Code!
Ribosomes translate genetic information encoded in the mRNA
into protein building blocks (chains of amino acids)
Protein folds into 3D active structure
Protein functions in cell
DNA Code Is Copied into a “Portable” Code: mRNA
RNA POLYMERASE (RNAP: COPIES DNA INTO mRNA)
DNA
DNA
C U A A
G A T T
3’
Note: DNA
base-pairs between
backbone strands
are not shown here
mRNA
mRNA: AUGGAGUACUAAUAUGUAAAAAAAAAAAAAAAAAAA-3’
DNA: ATGGAGTACTAATATGT-3’
TACCTCATGATTATACA-5’
MFHMAF2001
RNA Code has Different Alphabet Than DNA Code
(RNA has U instead of T)
DNA:
ATGGAGTACTAATATGT-3’
TACCTCATGATTATACA-5’
DNA strand has “T”
DNA Base-Pair
3’-TACCTCATGATTATACA-5’DNA STRAND
AUGGAGUACUAAUAUGU mRNA copied from DNA
RNA has U instead of T
When DNA is copied into mRNA (transcription),
U is incorporated into mRNA in place of T
DNA Strands “Unzip” so the DNA Letters Can be “Read”
-ATGGAGTACTAATATGT-TACCTCATGATTATACA-
DOUBLE-STRANDED DNA
(Region from Chromosome)
DNA STRANDS SEPARATE
-TACCTCATGATTATACAAUGGAGUACUAAUAUGU mRNA copied from DNA
DNA STRANDS COME BACK
TOGETHER BY BASE-PAIRING
-ATGGAGTACTAATATGT-TACCTCATGATTATACADNA HELIX STAYS IN NUCLEUS
+
AUGGAGUACUAAUAUGU mRNA
mRNA GOES TO CYTOPLASM
TO PROTEIN FACTORY
Genetic Code is Written in 3-Letter DNA Words (Codons)
-TACCTCATGATTATACA- DNA(DNA strands separated)
-AUGGAGUACUAAUAUGU mRNA (copied from DNA)
5’-AUGGAGUACUAAUAUGU mRNA
5’-AUG GAG UAC UAA UAU mRNA
mRNA code “read”
by ribosome in
TANDEM triplets
called codons.
Codon adaptors
convert RNA letters
CODON MEANINGS:
into the correct
•A “START PROTEIN” SIGNAL: AUG
amino acid building
•A “STOP PROTEIN” SIGNAL: UAA, UGA, UAG
blocks in the protein
•An amino acid building block of a protein
•Codons identified in the Genetic Code Table chain.
The Universal Genetic Code Table
Name of Building
Block Amino Acid:
Phe=Phenylalanine
Leu=Leucine
Ile=Isoleucine
AUG CODON:
Signal to start
making the protein.
http://anx12.bio.uci.edu/~hudel/bs99a/lecture20/lecture1_6.html
STOP
Codons:
UAA
UAG
UGA
Genetic Code is Written in 3-Letter DNA Words
-TACCTCATGATTATACA- DNA STRAND
AUGGAGUACUAAUAUGU mRNA copied from DNA
mRNA code is “read” in TANDEM CODONS
5’-AUGGAGUACUAAUAUGU mRNA
5’-AUG GAG UAC UAA UAU mRNA
Met-Glu-Tyr-STOP
N Met Glu Tyr C
A SHORT PROTEIN IS A PEPTIDE
CODON MEANINGS:
•“START PROTEIN HERE”: AUG (START) Methionine (Met)
•“STOP PROTEIN HERE”: UAA, UGA, UAG
•Amino acid building blocks: N-Met-Glu-Tyr-C
•Codons are identified in the Genetic Code Table
Proteins Have Two Ends: The N- And C- Termini
5’-AUGGAGUACUAAUAUGU mRNA
5’-AUG GAG UAC UAA mRNA
Met-Glu-Tyr-STOP
N Met Glu Tyr C
A short protein
(peptide) has only a
few amino acid (aa)
building blocks.
The first aa in the
chain (usually Met)
(AUG) is at the Nterminus.
The final aa added
to the chain is the
C-terminus.
Ribosome Protein Factory Reads the RNA Codons
RNA is Copied From DNA (Gene)
NUCLEUS
GENE DNA UNZIPS
mRNA
Protein Synthesis
amino
acid
N
Protein
Chain
Folds
AA
mRNA
Transfer RNA (tRNA): Matches mRNA codon
with correct amino acid building block
MFHMAF2001
Proteins Fold into 3D Structures
Proteins live in a watery environment (living organisms!).
• Chemical parts that hate water fold on inside of protein.
• Chemical parts that love water go to the outside surface of protein.
• Surface of the folded protein interacts with proteins, DNA, RNA, etc.
Polar
“Pocket”
C
Small Folded
Protein
Legend
N
Hates Water
Likes Water
Hydrophobic
“Pocket”
Likes Water
Likes Water
Different Protein Chains Fold to Make Proteins
with Different 3D Shapes and Biological Functions
Protein #1
Protein #2
Protein #3
Protein #2
Protein #1
Human proteins have
20 different amino
acid building blocks
Protein #3
Molecular Structures Related to Protein Function in the Cell
EF Hand Binds Calcium
DNA Intersection:
Holliday Junction
“Syringe”
Channel
Basket
One Gene-One Protein
Archibald Garrod (1902) described
alkaptonuria, a hereditary disorder as an
“inborn error of metabolism”.
 Proposed that mutations cause specific
biochemical defects.
 Alkaptonuria defect is dark urine.

A DNA Spelling Mistake Can Alter the Protein Chain
START ADD
ADD
ADD
ADD
ADD
ADD
ADD
STOP
ATG TTC AGG CCA AAT TTT GTC GCG UAA GGA ATT
Spelling Mistake
The DNA “word” TTC is changed to TTT
ATG TTT AGG CCA AAT TTT GTC GCG
TTC to TTT spelling change causes a different protein building
block to be inserted in the second position. That is all it takes.
ADD = Codon specifies the amino acid specified by 3-letter “word”
ATG/AUG = Codon specifies start and methionine (met)
UAA = STOP adding amino acids to protein chain
A Mutation is a DNA “Spelling Mistake”
Mutant Genes Encode Defective Proteins:
(1) WILDTYPE
Example: AAA GCT ACC TAT
TTT CGA TGG ATA
Phe Arg Trp Ile
PROTEIN:
WT FUNCTION
(2) MUTANT
AAA GCT ATC TAT
TTT CGA TAG ATA
Phe Arg Stop
UAG
NO FUNCTION
(1) Normal DNA and amino acid sequence makes a wild-type protein.
(2) Mutation in DNA changes Trp to Stop to make a short, mutant protein.
Mutations in DNA can be Caused by:
• Mistakes made when the DNA is replicated (wrong base inserted)
• Ultra violet (UV) light and ionizing radiation (X-rays) damage DNA
• Environmental chemical carcinogens can damage DNA
• Other factors
DNA Technology: The Awesome Skill, I E Alcamo, Harcourt Academic Press, 2001
Misspelled Genes: 3 Possible Outcomes
DNA
A misspelled gene
Cell may not
be able to
follow
damaged
instruction
Cell does not
make the
protein
OR
X
X
Damaged
protein is
made
Damaged
protein may or
may not be able
to function in
the cell.
OR
Spelling
error may be
harmless
Functional
protein made
by the cell
DNA is Stored in the Nucleus (in Complex Cells)
Complex cells have compartments, bacterial cells do not.
Minimalist Complex Cell
DNA
RNA
CELL MEMBRANE
Controls entry and exit from cell
NUCLEUS
Cell Control Centercontains DNA, acivation of gene send
RNA copies out into the cytoplasm.
This is called gene expression.
CYTOPLASM
The area and material inside the
cell, but outside the nucleus and
other comparments
RIBOSOMES
Make proteins from RNA instructions
Every Cell Has a Complete Copy of Genome DNA:
•
Virtually every cell in your body contains its own
complete copy of all your DNA
•
A single, complete copy of an organism’s DNA is
called its genome
•
The genome is a set of instructions, like a master
plan, written in a molecular language, using DNA
instead of paper and ink
•
Therefore, each cell in your body has a copy of your
genome, which is, in essence, a master plan for
making you.
But Most of My Cells Don’t Make Melanin-- Right?
How BIG is 3.2 Billion DNA Letters?
Human Genome Has 3.2 Billion
DNA Letters: 3,200,000,000 bp
Human Genome
3.2 billion (3.2 x 109) is the same as:
• 200 (1000 pages each) New York
City telephone books
• 3 Gigabyte computer hard drive
• a person typing 60 words/minute
for 8 hours/day, would take more
than 50 years to type the entire
human genome sequence
• placed end-to-end the DNA in one
human cell extends almost 6 feet
Genome Facts: NOVA Online
Access Excellence Cell to Chromosome to DNA
One DNA
base-pair
How Big are Plant Genomes?
Human Genome Has 3.2 Billion
DNA Letters: 3200 million bp
Plant Genome
Maize (Corn) Genome has 2.5
Billion DNA Letters: 2500 million bp
Arabidopsis Genome has 125
million bp
Rice Genome has 430 million bp
Wheat Genome has 16,000
million bp
One DNA
base-pair
Nucleus Executes The Genome Master Plan
PLANT CELL:
Genome
Master Plan is
Executed: CHLOROPLAST
CELL WALL
(1) DNA is copied into RNA
code (mRNA)
(2) mRNA is transported to the
cytoplasm
(3) Translate mRNA code into
chain of protein building
blocks at the ribosome.
NUCLEUS
DNA
mRNA
(2)
(3)
mRNA
PROTEIN
mRNA
NUCLEAR
PORE
RIBOSOME
CYTOPLASM
CYTOPLASM
CELL MEMBRANE
Danny Schnell, BMB
(1)
DNA is Packaged Into Chromosomes
DNA double helix
GENE (blue)
Several GENES
along a length of DNA
DNA is coiled around proteins
(more on this later)
Small region of
“unwrapped”
chromosome
Loosely wrapped DNA
in chromosome
Tightly wrapped
chromosome
Adapted from
Alberts et al.
Molecular Cell Biology
How Many Chromosomes Are There?
Bacteria usually have one circular
chromosome and no nucleus
Organisms with nuclei have
variable numbers of chromosomes
depending on the species:
• Mosquito 6
• Chimpanzees 48
• Goldfish 94
How Many Chromosomes Are There?
Some plants have few
chromosomes like Arabidopsis.
Others, like sugarcane, have many.
Wheat
42
Rice
24
Arabidopsis
10
Sugarcane
+100
Maize
20
Potato
48
Tomato
24
Cabbage
20
Carrot
18
Chromosomes are Dynamic Structures
Human Chromosomes
CONDENSED
EXTENDED
Metaphase
Chromosome
Fruit Fly
DNA Discovery
Discover DNA: It is Changing OUR Lives…
•Human Cloning
(imagine dozens of identical siblings!!)
•Designer Babies
(and all of them “perfect”!?!)
•Stem Cells
(can we help paralyzed people to walk?)
•Gene Therapy
(can we fix “broken” genes?)
•DNA Fingerprinting
(nowhere to hide??!!)
Some Questions Students May Have?
Most of us know we have DNA and genes…
What are genes and how much do they influence us?
What do genes and DNA actually do?
What is a genome?
What is the Human Genome Project?
Will the Human Genome Project affect me?
Our DNA Story
Variations on the Human Theme!
People look very different from each other.
Yet we all have features in common, 2 arms, 2 legs, one
head, one nose, etc.
Traits are Inherited
Traits are characteristics that vary among individuals.
Simple trait:
•Eye color: Blue, brown, green
•Seed coat color
Complex traits:
•Blood types: A, B, AB, O
•Plant height.
•Plant disease resistance.
Connection between traits and genes: TRAITS are inherited from parents
through GENES!
Genes are Responsible for the Traits You Inherit
Genes determine:
•physical traits and influence personality
•biological characteristics such as blood type
•level of health risk (heart disease, stroke, alcoholism, Alzheimer’s)
•specific genetic diseases (sickle cell, hemophilia, cancer, etc.)
•inherited traits that are passed on to your biological children
However: the environment always affects the result of
genetic inheritance.
Example: genes for growth are influenced by nutrition
available during child development