Download From Genetics to DNA

From Genetics to DNA
Extracting DNA modified from: http://learn.genetics.utah.edu/units/activities/extraction/
Edible model of DNA: http://gslc.genetics.utah.edu
http://en.wikipedia.org/wiki/DNA
http://en.wikipedia.org/wiki/DNA_sequence
http://psyche.uthct.edu/shaun/SBlack/geneticd.html
Students will:
 Build a model of DNA
 Discuss the mechanisms for translation
 Examine simulated sequences of DNA
 Extract, cleave the proteins, isolate and precipitate out DNA, making it visible
 Simulate restricting DNA
 Simulate running this DNA in gel electrophoresis
 Determine which of the three suspects in this simulation is implicated
 Examine a variety of pictures of gels to determine paternity, and eliminate or implicate
suspects in a crime scene
Benchmarks:
Life Science
CCG Organisms: Understand the characteristics, structure, and functions of
organisms.
SC.03.LS.01
Recognize characteristics that are similar and different
between organisms.
SC.05.LS.01
Group or classify organisms based on a variety of
characteristics.
SC.05.LS.01.01 Classify a variety of living things into groups using
various characteristics.
CCG Heredity: Understand the transmission of traits in living things.
SC.03.LS.03
Describe how related plants and animals have similar
characteristics.
SC.05.LS.04
Describe the life cycle of an organism.
SC.05.LS.04.01 Describe the life cycle of common organisms.
SC.05.LS.04.02 Recognize that organisms are produced by living
organisms of similar kind, and do not appear
spontaneously from inanimate materials.
SC.08.LS.03
Describe how the traits of an organism are passed from
generation to generation.
SC.08.LS.03.01 Distinguish between asexual and sexual
reproduction.
SC.08.LS.03.02 Identify traits inherited through genes and those
resulting from interactions with the environment.
SC.08.LS.03.03 Use simple laws of probability to predict patterns of
heredity with the use of Punnett squares.
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CCG Diversity/Interdependence: Understand the relationships among living
things and between living things and their environments.
SC.08.LS.05
Describe and explain the theory of natural selection as a
mechanism for evolution.
SC.08.LS.05.01 Identify and explain how random variations in
species can be preserved through natural selection.
Materials:
 Permanent
 Scissors
 Copies of DNA
 Copies of DNA sequencing
 Copies DNA codes for proteins
 Blender
 Ice bucket
 Measuring cup
 1/8 Measuring spoon
 Strainer
 Clean empty milk jug (for water)
 Copies of gel electrophoresis results
 Gel for electrophoresis model
 Copies of gel photographs
 DNA models (optional)

Consumable
 4 red licorice sticks
 2 black licorice stick
 color mini marshmallows
 white mini marshmallows
 wax paper
 toothpicks
 Color paper for copies of proteins
 Copies of DNA sequence
 Copies of restriction enzymes
 Cups
 Centrifuge tubes
 Isopropyl alcohol (at least 95%)
 Ice
 Salt
 Liquid dish soap
 Unseasoned meat tenderizer
 Dried peas
 Sterile swabs
 Glue sticks
 Masking tape or small labels
 Permanent markers – fine point
 Copies of Amino Acid circles
Discussion:
This lesson plan is part two of three-parts in understanding DNA and how DNA fingerprints
work. In the genetics lab, your students looked at variation in individuals to cement their
foundation for understanding the how (alleles) behind individual variation. In this class, there
are 4 activities to help students conceptualize DNA both as a model and actually seeing it, and
that variation is caused by a change in the sequence. In addition, students will model how
scientists use DNA sequences in solving crimes. Examining gels displaying mother, child and
potential fathers reinforce student understanding of genetics from the prior lesson.
Overview of Activities:
Activity 1
Students will continue their understanding of DNA through building an edible model of the
DNA, an edible mRNA, and build a protein from the mRNA. The structure of DNA is
discussed, being comprised of 4 bases, Adenine, Cytosine, Guanine, and Thymine, and the AT
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and GC pairing of them. The sequences of these four bases are a code that translates into amino
acids, building proteins that enable a cell to function properly. There are sequences of DNA that
are highly conserved (i.e. 16S and 16S rRNA), and portions of these sequences are identical
from bacteria to us. These code for very important functions, like protein building.
Activity 2
Students will extract and isolate DNA from their cheek cells by breaking membranes, cleaving
histones, allowing the cellular debris to settle, and precipitating the DNA in a layer between
water and ice cold isopropyl alcohol, concentrating it so that it is visible to the naked eye. This
extraction-cleaving-isolation-precipitation is done using common household materials.
Activity 3
There are sections in our DNA that do not code for any gene. These are referred to as “junk”
DNA. There is a lot of variation in the DNA in these regions. In fact there is so much variation,
we can use them to identify individuals. Students then examine paper sequences for 3
individuals and a crime scene. The students add a paper restriction enzyme that cleaves the
DNA in specific locations. The students then run their paper DNA out on a table gel
electrophoresis, and determine which of the three is the culprit.
Activity 4
Students practice what they have learned by examining photographs of different crime scene
gels. From these gels, they can identify the culprit. In addition, students can examine paternity
gels to identify that the alleles come from both their mother and their father.
Set-up for Class:
Students work with a partner, but everyone
participates with their own analysis
 Set out for each pair of students:
 copies in page protectors of DNA
 copies in page protectors of
sequencing DNA
 copies in page protectors of DNA
codes for proteins
 copies of Crime Scene DNA gels
 copies of DNA paternity gels
 ~36 toothpicks
 2 large sheets wax paper
 2 pair scissors
 color disk “amino acids”
 Student work copies of Crime
Scene DNA sequences
 Student work copies of Crime
Scene restriction enzymes
 2 Student “gel”
 2 cups (3 ounce)
 2 centrifuge tubes



permanent markers
2 sterile swabs
Put in convenient location but away
from students:
 Red licorice
 Black licorice
 White mini marshmallows
 Color mini marshmallows
 Masking tape (or little labels)
 DNA extraction chemical center
o Salt
o Dish washing soap
o Meat tenderizer
o Bucket with ice
o Isopropyl alcohol buried in
the ice
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DNA Structure Activity 1
Supplies:
 Per student:
 2 pieces of red licorice
 17 toothpicks
 9 pink marshmallows (Thymine)
 9 white marshmallows (Uracil)
 18 yellow marshmallows (Cytocine)
 18 green marshmallows (Adenine)
 18 orange marshmallows (Guanine)
 Masking Tape or small labels
 Scotch Tape
 Permanent markers – fine point
 1 piece black licorice
 2 of each of the Amino Acid circles
Discussion:
Structure
Deoxyribonucleic acid (DNA) is a nucleic acid that contains
the genetic instructions used in the development and
functioning of all known living organisms. The main role of
DNA molecules is the long-term storage of information and
DNA is often compared to a set of blueprints, since it
contains the instructions needed to construct other
components of cells, such as proteins and RNA molecules.
The DNA segments that carry this genetic information are
called genes, but other DNA sequences have structural
purposes, or are involved in regulating the use of this genetic
information.
Major Groove
Chemically, DNA is a long polymer of simple units called
Minor Groove
nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds.
Attached to each sugar is one of four types of molecules called bases. It is the sequence of these
four bases along the backbone that encodes information. This information is read using the
genetic code, which specifies the sequence of the amino acids within proteins. The code is read
by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.
Most of these RNA molecules are used to synthesize proteins, but others are used directly in
structures such as ribosomes and spliceosomes.
Within cells, DNA is organized into structures called chromosomes. These chromosomes are
duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms such
as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such
as bacteria it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such
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as histones compact and organize DNA, which helps control its interactions with other proteins
and thereby control which genes are transcribed.
Physical and chemical properties
DNA is a long polymer made from repeating units called nucleotides. The DNA chain is 22 to
26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit is 3.3 Ångstroms
(0.33 nanometres) long. Although each individual repeating unit is very small, DNA polymers
can be enormous molecules containing millions of nucleotides. For instance, the largest human
chromosome, chromosome number 1, is 220 million base pairs long.
In living organisms, DNA does not usually exist as a single molecule, but instead as a tightlyassociated pair of molecules. These two long strands entwine like vines, in the shape of a double
helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which
holds the chain together, and a base, which interacts with the other DNA strand in the helix. In
general, a base linked to a sugar is called a nucleoside and a base linked to a sugar and one or
more phosphate groups is called a nucleotide. If multiple nucleotides are linked together, as in
DNA, this polymer is referred to as a polynucleotide.
The backbone of the DNA strand is made from alternating phosphate and sugar residues. The
sugar in DNA is 2-deoxyribose, which is a pentose (five carbon) sugar. The sugars are joined
together by phosphate groups that form phosphodiester bonds between the third and fifth carbon
atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In
a double helix the direction of the nucleotides in one strand is opposite to their direction in the
other strand. This arrangement of DNA strands is called antiparallel. The asymmetric ends of
DNA strands are referred to as the 5′ (five prime) and 3′ (three prime) ends. One of the major
differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the
alternative pentose sugar ribose in RNA.
The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two
strands. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G)
and thymine (T). These four bases are shown below and are attached to the sugar/phosphate to
form the complete nucleotide, as shown for adenosine monophosphate.
These bases are classified into two types; adenine and guanine are fused five- and six-membered
heterocyclic compounds called purines, while cytosine and thymine are six-membered rings
called pyrimidines. A fifth pyrimidine base, called uracil (U), usually takes the place of thymine
in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually
found in DNA, occurring only as a breakdown product of cytosine, but a very rare exception to
this rule is a bacterial virus called PBS1 that contains uracil in its DNA. In contrast, following
synthesis of certain RNA molecules, a significant number of the uracils are converted to
thymines by the enzymatic addition of the missing methyl group. This occurs mostly on
structural and enzymatic RNAs like transfer RNAs and ribosomal RNA.
The double helix is a right-handed spiral. As the DNA strands wind around each other, they
leave gaps between each set of phosphate backbones, revealing the sides of the bases inside (see
animation). There are two of these grooves twisting around the surface of the double helix: one
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groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide. The
narrowness of the minor groove means that the edges of the bases are more accessible in the
major groove. As a result, proteins like transcription factors that can bind to specific sequences
in double-stranded DNA usually make contacts to the sides of the bases exposed in the major
groove.
Base pairing
Each type of base on one strand forms a bond with just
one type of base on the other strand. This is called
complementary base pairing. Here, purines form
hydrogen bonds to pyrimidines, with A bonding only
to T, and C bonding only to G. This arrangement of
two nucleotides binding together across the double
helix is called a base pair. In a double helix, the two
strands are also held together via forces generated by
the hydrophobic effect and pi stacking, which are not
influenced by the sequence of the DNA. As hydrogen
bonds are not covalent, they can be broken and
rejoined relatively easily. The two strands of DNA in a
double helix can therefore be pulled apart like a zipper,
either by a mechanical force or high temperature. As a
result of this complementarity, all the information in
the double-stranded sequence of a DNA helix is
duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific
interaction between complementary base pairs is critical for all the functions of DNA in living
organisms.
The two types of base pairs form different numbers of hydrogen bonds, AT forming two
hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). The GC base pair is
therefore stronger than the AT base pair. As a result, it is both the percentage of GC base pairs
and the overall length of a DNA double helix that determine the strength of the association
between the two strands of DNA. Long DNA helices with a high GC content have strongerinteracting strands, while short helices with high AT content have weaker-interacting strands.
Parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in
bacterial promoters, tend to have sequences with a high AT content, making the strands easier to
pull apart. In the laboratory, the strength of this interaction can be measured by finding the
temperature required to break the hydrogen bonds, their melting temperature (also called Tm
value). When all the base pairs in a DNA double helix melt, the strands separate and exist in
solution as two entirely independent molecules. These single-stranded DNA molecules have no
single common shape, but some conformations are more stable than others.
Sense and antisense
A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy
that is translated into protein. The sequence on the opposite strand is complementary to the sense
sequence and is therefore called the "antisense" sequence. Since RNA polymerases work by
making a complementary copy of their templates, it is this antisense strand that is the template
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for producing the sense messenger RNA. Both sense and antisense sequences can exist on
different parts of the same strand of DNA (i.e. both strands contain both sense and antisense
sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the
functions of these RNAs are not entirely clear. One proposal is that antisense RNAs are
involved in regulating gene expression through RNA-RNA base pairing.
A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the
distinction made above between sense and antisense strands by having overlapping genes. In
these cases, some DNA sequences do double duty, encoding one protein when read 5′ to 3′ along
one strand, and a second protein when read in the opposite direction (still 5′ to 3′) along the other
strand. In bacteria, this overlap may be involved in the regulation of gene transcription, while in
viruses, overlapping genes increase the amount of information that can be encoded within the
small viral genome. Another way of reducing genome size is seen in some viruses that contain
linear or circular single-stranded DNA as their genetic material.
Supercoiling
The secondary structure of DNA is the helices. DNA can be twisted like a rope in a process
called DNA supercoiling. With DNA in its "relaxed" state, a strand usually circles the axis of the
double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more
tightly or more loosely wound. If the DNA is twisted in the direction of the helix, this is positive
supercoiling, and the bases are held more tightly together. If they are twisted in the opposite
direction, this is negative supercoiling, and the bases come apart more easily. In nature, most
DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases.
These enzymes are also needed to relieve the twisting stresses introduced into DNA strands
during processes such as transcription and DNA replication.
Mutations
DNA can be damaged by many different sorts of mutagens. These include oxidizing agents,
alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and xrays. The type of DNA damage produced depends on the type of mutagen. For example, UV
light mostly damages DNA by producing thymine dimers, which are cross-links between
adjacent pyrimidine bases in a DNA strand. On the other hand, oxidants such as free radicals or
hydrogen peroxide produce multiple forms of damage, including base modifications, particularly
of guanosine, as well as double-strand breaks. It has been estimated that in each human cell,
about 500 bases suffer oxidative damage per day. Of these oxidative lesions, the most dangerous
are double-strand breaks, as these lesions are difficult to repair and can produce point mutations,
insertions and deletions from the DNA sequence, as well as chromosomal translocations.
Many mutagens intercalate into the space between two adjacent base pairs. Intercalators are
mostly aromatic and planar molecules, and include ethidium, daunomycin, doxorubicin and
thalidomide. In order for an intercalator to fit between base pairs, the bases must separate,
distorting the DNA strands by unwinding of the double helix. These structural changes inhibit
both transcription and DNA replication, causing toxicity and mutations. As a result, DNA
intercalators are often carcinogens, with benzopyrene diol epoxide, acridines, aflatoxin and
ethidium bromide being well-known examples. Nevertheless, due to their properties of
inhibiting DNA transcription and replication, they are also used in chemotherapy to inhibit
rapidly-growing cancer cells.
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Overview of biological functions
DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in
prokaryotes. The set of chromosomes in a cell makes up its genome; the human genome has
approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The information
carried by DNA is held in the sequence of pieces of DNA called genes. Transmission of genetic
information in genes is achieved via complementary base pairing. For example, in transcription,
when a cell uses the information in a gene, the DNA sequence is copied into a complementary
RNA sequence through the attraction between the DNA and the correct RNA nucleotides.
Usually, this RNA copy is then used to make a matching protein sequence in a process called
translation which depends on the same interaction between RNA nucleotides. Alternatively, a
cell may simply copy its genetic information in a process called DNA replication. The details of
these functions are covered in other articles; here we focus on the interactions between DNA and
other molecules that mediate the function of the genome.
Genome structure
Genomic DNA is located in the cell nucleus of eukaryotes, as well as small amounts in
mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped
body in the cytoplasm called the nucleoid. The genetic information in a genome is held within
genes. A gene is a unit of heredity and is a region of DNA that influences a particular
characteristic in an organism. Genes contain an open reading frame that can be transcribed, as
well as regulatory sequences such as promoters and enhancers, which control the expression of
the open reading frame.
In many species, only a small fraction of the total sequence of the genome encodes protein. For
example, only about 1.5% of the human genome consists of protein-coding exons, with over
50% of human DNA consisting of non-coding repetitive sequences. The reasons for the
presence of so much non-coding DNA in eukaryotic genomes and the extraordinary differences
in genome size, or C-value, among species represent a long-standing puzzle known as the "Cvalue enigma." However, DNA sequences that do not code protein may still encode functional
non-coding RNA molecules, which are involved in the regulation of gene expression.
Transcription and translation
A gene is a sequence of DNA that contains genetic information and can influence the phenotype
of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger
RNA sequence, which then defines one or more protein sequences. The relationship between the
nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the
rules of translation, known collectively as the genetic code. The genetic code consists of threeletter 'words' called codons formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT).
In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This
RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the
messenger RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter
combinations, there are 64 possible codons (43 combinations). These encode the twenty standard
amino acids, giving most amino acids more than one possible codon. There are also three 'stop'
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or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG
codons.
Tertiary Structure of DNA
Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein
interactions. Within chromosomes, DNA is held in complexes with structural proteins. These
proteins organize the DNA into a compact structure called chromatin. In eukaryotes this structure
involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes
multiple types of proteins are involved. The histones form a disk-shaped complex called a
nucleosome, which contains two complete turns of double-stranded DNA wrapped around its
surface. These non-specific interactions are formed through basic residues in the histones making
ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely
independent of the base sequence. Chemical modifications of these basic amino acid residues
include methylation, phosphorylation and acetylation. These chemical changes alter the strength
of the interaction between the DNA and the histones, making the DNA more or less accessible to
transcription factors and changing the rate of transcription. Other non-specific DNA-binding
proteins found in chromatin include the high-mobility group proteins, which bind preferentially
to bent or distorted DNA. These proteins are important in bending arrays of nucleosomes and
arranging them into more complex chromatin structures.
In contrast, other proteins have evolved to specifically bind particular DNA sequences. The most
intensively studied of these are the various classes of transcription factors, which are proteins
that regulate transcription. Each one of these proteins bind to one particular set of DNA
sequences and thereby activates or inhibits the transcription of genes with these sequences close
to their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA
polymerase responsible for transcription, either directly or through other mediator proteins; this
locates the polymerase at the promoter and allows it to begin transcription. Alternatively,
transcription factors can bind enzymes that modify the histones at the promoter; this will change
the accessibility of the DNA template to the polymerase.
As these DNA targets can occur throughout an organism's genome, changes in the activity of one
type of transcription factor can affect thousands of genes. Consequently, these proteins are often
the targets of the signal transduction processes that mediate responses
to environmental changes or cellular differentiation and development.
The specificity of these transcription factors' interactions with DNA
come from the proteins making multiple contacts to the edges of the
DNA bases, allowing them to "read" the DNA sequence. Most of these
base-interactions are made in the major groove, where the bases are
most accessible.
Directions:
 Students work with a partner. Each partner needs to select
a different sequence. The sequences are included in the
picture of the double helix picture in the page protector.
 One partner needs to pick:
o DNA Sequence 1 – T A C G T A T G A A A C
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

The other partner needs to pick:
o DNA Sequence 2 – T G G T T T A G A A T T
To assemble one side of the DNA molecule:
 A piece of red licorice will form the backbone and marshmallows will be the
chemical bases.
 Place a marshmallow on the end of a toothpick so that the point of the toothpick
goes all the way through.
 Anchor the toothpick into the licorice backbone. Refer to the table with the
sequence information for the color of marshmallow that represents the chemical
bases in your sequence.
 Label the backbone. With a marker or pen and small stickers, label your licorice
backbone “DNA- 1” or “DNA-2” depending on which sequence you used. Write
the label on the left end of the licorice.
 Match the chemical base pairs. Place the color marshmallow for the matching
chemical base on the other end of each
toothpick. Remember that A always pairs with
T and C always pairs with G!
 To complete your DNA model, attach the other
backbone (red licorice stick) so your model
looks like a ladder.
 Carefully twist your DNA molecule so that it
Marshmallow Toothpick Licorice Stick
looks like a double helix.
Transcription:
 The four chemical bases in DNA (A, C, G, and T) create a code. Cells “read” this
DNA code to make proteins, the building blocks of all organisms. This is done in two
steps:
 Copying the directions – Transcription
 Reading the copy to string together the small molecules (amino acids) that make
up a protein – Translation.
 Making a Copy of DNA – Transcription
 Cells read DNA in small portions (genes) to create a protein. To do this, the cell
must first make a copy of the gene’s code to send to the protein-building
machinery. This process is called transcription.
Using the following materials, follow the steps
below to see how this is done.
 Transcription
 RNA is single stranded and only “reads” DNA
from one strand.
 Unzip your DNA. In order to make this copy, the
chemical bases forming the rungs of the DNA
ladder must be separated. Do this by cutting or
breaking in the middle the toothpicks in your
model to separate the chemical bases and unzip
the DNA ladder. Break the toothpicks between
the two marshmallows.
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


Set aside the unlabeled backbone (with chemical bases attached) aside.
Begin to form your mRNA strand. The exposed chemical bases of the unzipped
DNA are used to make the copy. This copy is called messenger RNA (mRNA).
The mRNA molecule is also made of a backbone and the same chemical bases as
DNA. There is one exception however – instead of Thymine (T), mRNA uses
Uracil (U). The chemical bases in mRNA form pairs in the same way as DNA:
o Adenine (A) binds with Uracil (U)
o Guanine (G) binds with Cytosine (C).
 Place your backbone labeled “DNA-1” or “DNA-2” (depending on which you
used to make your model) in front of you. Follow the rules of base pairing to
make your mRNA copy of the DNA code by lining up colored marshmallows
with their appropriate match. The chemical bases of mRNA are also attached to a
backbone as in DNA.
 Attach the new chemical bases to a piece of black licorice backbone using
toothpicks cut or broken in half. This forms a new mRNA copy of your DNA
strand.
 • Label this new strand mRNA-1 or mRNA-2 (the same number as your DNA
strand) on the left end of the backbone.
Translation
 The mRNA copy of DNA is essentially a recipe for assembling a protein.
Proteins are built from small molecules called amino acids. When the mRNA
copy is sent to the protein-building machinery it is read and the appropriate amino
acids are assembled. This process is called translation.
 Begin to create your protein. mRNA is read in groups of three chemical bases.
Each group of three tells the cell which amino acid to assemble. In other words,
each group of three is a “code” for a particular amino acid.
 You and your partner will need to work together to build your complete protein.
Between the two of you, you will have both the mRNA-1 and mRNA-2.
 Place both strands of mRNA end-to-end on the table in front of you, with the
mRNA-1 strand on the left.
 Look at the first 3 chemical bases on the left end of your mRNA strand.
 Use the Amino Acid Key to determine which amino acid these 3 chemical bases
code.
 Place the colored circle cut-out representing that amino acid on the table directly
below the three chemical bases.
 Repeat Step 1 for each group (or code) of three chemical bases on the mRNA
strand.
 Now you have a protein!
 You may take home your DNA and mRNA models. Yummy!
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Extracting DNA Activity 2
Supplies:
 Craft sticks or swab (1
per student)
 Cup (students can use the
cup for their
marshmallows from
Activity 1)
1) Salt
 Water
 Liquid dish soap
 Ice cold 95-99%
isopropyl alcohol
 Centrifuge tubes
 Permanent marker
Discussion:
Extracting DNA, amplifying
DNA, using restriction
enzymes and cleaving DNA
are different techniques
which scientists use to study
evolution, medicine, and
forensic science (to name just three). The focus of this lesson is the location of DNA within the
cell. Cells are enclosed in membranes. In order to release the DNA, these membranes need to
be broken without damaging the DNA. We do this with soap. Think about why you use soap to
wash dishes or your hands. To remove grease and dirt, right? Soap molecules and grease
molecules are made of two parts:
 Heads, which like water.
 Tails, which hate water.
Both soap and grease molecules organize themselves in bubbles (spheres) with their heads
outside to face the water and their tails inside to hide from the water. When soap comes close to
grease, their similar structures cause them to combine, forming a greasy soapy ball. A cell's
membranes have two layers of lipid (fat) molecules with proteins going through them. When
soap comes close to the cell, it captures the lipids and proteins. After adding the detergent, what
do you have in your pea soup? (Free floating DNA from the nucleus still with the attached
histone proteins and mitochondria.)
Salt was added to the pea (or spit). DNA is negatively charged. The salt provides the DNA with
positively charged sodium ions to help neutralize it.
We add the meat tenderizers to cut the proteins away from the DNA. The DNA is wrapped
around histones, which are proteins organizing DNA.
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There seem to be a wide variety of answers to exactly the mechanisms with precipitate the DNA,
and I have never been much satisfied with them. Perhaps they just seem too short – like this is a
trivial question. Here is the best answer that I have found:
 The alcohol is less dense than water, and DNA is also less dense than water. The DNA is
neutrally buoyant in the alcohol. DNA is polar and alcohol is non-polar. The
combination of these factors precipitate the DNA out of the alcohol, and keep it
suspended at that layer.
 I cannot locate any reasoning behind the ice-cold alcohol. When I am asked, I tell the
students that I haven’t found the answer yet. Questions drive science, and we discuss the
process of science.
Directions:
1) Label your centrifuge tube with your initials.
2) Fill the centrifuge tube about 1/2 full of water.
3) Pour this into your 3 oz cup.
4) Using the swab, scrap the inside of your mouth, collecting loose cheek cells. Scrap hard
enough to get as many as possible, but not hard enough to hurt yourself.
5) Using the water in your 3 oz. cup, swish the water in your mouth, and spit it back into your
cup.
6) Form a little spout with the cup and pour the water and spit/cheek cell solution into the
centrifuge tube.
7) Put the swab into the tube and swish to remove the cells from the swab into the water.
8) Add a pinch of salt to the tube and gently swirl to mix. Be careful! If you stir too hard, you'll
break up the DNA, making it harder to see. (You can put on the lid of the tube, and
GENTLY rock it back and forth.)
9) Add 2 drops of liquid soap and gently swirl to mix. Try not to form bubbles. Be careful! If
you stir too hard, you'll break up the DNA, making it harder to see. (You can put on the lid
of the tube, and GENTLY rock it back and forth.)
10) Add a pinch of enzymes to the tube and gently swirl to mix. Be careful! If you stir too hard,
you'll break up the DNA, making it harder to see. (You can put on the lid of the tube, and
GENTLY rock it back and forth.)
a) Use meat tenderizer for enzymes. If you can't find tenderizer, try using pineapple juice or
contact lens cleaning solution.
b) In this experiment, meat tenderizer acts as an enzyme to cut proteins just like a pair of
scissors.
11) Let the mixture sit for 10 minutes or more.
12) Tilt your test tube and slowly pour the ice cold alcohol (95% isopropyl or ethyl alcohol) into
the tube down the side so that it forms a layer on top of the pea mixture. Pour until you have
about the same amount of alcohol in the tube as your spit solution.
13) DNA will rise into the alcohol layer from the spit layer. You can use a wooden stick or other
hook to draw the DNA into the alcohol.
a) Alcohol is less dense than water, so it floats on top. Since two separate layers are formed,
all of the grease and the protein that we broke up in the first two steps and the DNA have
to decide: "Hmmm...which layer should I go to?"
13
i) This is sort of like looking around the room for the most comfortable seat. Some will
choose the couch, others might choose the rocking chair.
b) In this case, the protein and grease parts find the bottom, watery layer the most
comfortable place, while the DNA prefers the top, alcohol layer.
c) DNA is a long, stringy molecule that likes to clump together.

Now that you've successfully extracted DNA from one source, you're ready to experiment
further. Try these ideas or some of your own:
 Experiment with other DNA sources. Which source gives you the most DNA? How
can you compare them?
 Experiment with different soaps and detergents. Do powdered soaps work as well as
liquid detergents? How about shampoo or body scrub?
 Experiment with leaving out or changing steps. We've told you that you need each
step, but is this true? Find out for yourself. Try leaving out a step or changing how
much of each ingredient you use.

Do only living organisms contain DNA? Try extracting DNA from things that you think
might not have DNA.
Want to conduct more DNA extraction experiments? Try out different soaps and detergents. Do
powdered soaps work as well as liquid detergents?
14
Gel Electrophoresis Modeling Activity 3
Supplies:
 Permanent
 Scissors
 Paper gel for electrophoresis model
 Copies of DNA sequence
 Copies of restriction enzymes – different color
 Glue sticks
Discussion:
DNA-modifying enzymes
Nucleases and ligases
Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester
bonds. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called
exonucleases, while endonucleases cut within strands. The most frequently-used nucleases in
molecular biology are the restriction endonucleases, which cut DNA at specific sequences. For
instance, the EcoRV enzyme recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at
the vertical line. In nature, these enzymes protect bacteria against phage infection by digesting
the phage DNA when it enters the bacterial cell, acting as part of the restriction modification
system. In technology, these sequence-specific nucleases are used in molecular cloning and
DNA fingerprinting.
Because of their ability to cut DNA in predictable locations, they are commonly used in
forensice science, as well as many other commonly techniques.
Electropherogram printout from automated sequencer showing part of a DNA sequence
A DNA sequence or genetic sequence is a succession of letters representing the primary structure
of a real or hypothetical DNA molecule or strand, with the capacity to carry information.
The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand
- adenine, cytosine, guanine, thymine bases covalently linked to phospho-backbone. In the
typical case, the sequences are printed abutting one another without gaps, as in the sequence
AAAGTCTGAC, going from 5' to 3' from left to right. A succession of any number of
nucleotides greater than four is liable to be called a sequence. With regard to its biological
function, which may depend on context, a sequence may be sense or anti-sense, and either
coding or noncoding. DNA sequences can also contain "junk DNA."
Genetic (or DNA) Fingerprinting
Forensic scientists can use DNA in blood, semen, skin, saliva or hair at a crime scene to identify
a perpetrator. This process is called genetic fingerprinting, or more accurately, DNA profiling. In
15
DNA profiling, the lengths of variable sections of repetitive DNA, such as short tandem repeats
and minisatellites, are compared between people. This method is usually an extremely reliable
technique for identifying a criminal. However, identification can be complicated if the scene is
contaminated with DNA from several people. DNA profiling was developed in 1984 by British
geneticist Sir Alec Jeffreys, and first used in forensic science to convict Colin Pitchfork in the
1988 Enderby murders case. People convicted of certain types of crimes may be required to
provide a sample of DNA for a database. This has helped investigators solve old cases where
only a DNA sample was obtained from the scene. DNA profiling can also be used to identify
victims of mass casualty incidents.
Directions:











Students work in groups of 4.
Give each student one strip of DNA (from Suspect 1, Suspect 2, Suspect 3, or Crime
Scene.
Instruct each students to cut the DNA sequences and tape the for strips in sequence
together to make one long strand.
Students glue the restriction enzyme over the sequence whenever it matches. (Normally,
the restriction enzyme will seek out the complimentary strand. However in this model,
have the students match the sequence to eliminate any confusion. After this activity is
completed, then we discuss that the restriction enzyme would actually bond to the
complimentary DNA.)
Students cut their strands where indicated on each of the restriction enzymes.
Be very clear that the students MUST not contaminate their strands. They must keep
them separate and identified.
Direct the students to count the number of nucleotides in each fragment and writing this
number on the back.
The students fold their DNA to fit the well of the paper gel.
Note that the paper gel already has a ladder.
The students move their DNA fragments to the correct position (as indicated by the
ladder).
When completed, the gel should reveal which of the three suspects is the culprit.
16
Practice Reading Gels Activity 4
Supplies:
 Copies of DNA gel electrophoresis
Discussion:
Each gel is a mini mystery. By this time, students easily solve them. The paternity may take the
younger students a bit longer, but refer them back to their Marshmallow bugs and Punnett
squares. They receive only half of their genes from one parent. Half should match that parent.
They receive the other half from their other parent. That have should match the other parent.
Half of the parents, however, do not match the child. The child did not inherit those genes.
Directions:
 This is a quick – 2 to 15 minute activity.
 There are 5 pictures of crime scene gels,
 There is one nice diagram explanation paternity
 There are three paternity gels.
Note: There should be 6 copies of each of the gel photographs for the students. If you need to
replace any of them, the documents: “paternity.doc” and “suspect.doc” Gail should have them.
17
Green Green Green
Green Green Green
Green Green Green
Green Green Green
Green Green Green
Green Green Green
18
Green Yellow Yellow
Green Yellow Yellow
Green Yellow Yellow
Green Yellow Yellow
Green Yellow Yellow
Green Yellow Yellow
19
Green Yellow White
Green Yellow White
Green Yellow White
Green Yellow White
Green Yellow White
Green Yellow White
20
Green White Orange
Green White Orange
Green White Orange
Green White Orange
Green White Orange
Green White Orange
21
Yellow Green White
Yellow Green White
Yellow Green White
Yellow Green White
Yellow Green White
Yellow Green White
22
White Green Green
White Green Green
White Green Green
White Green Green
White Green Green
White Green Green
23
White Yellow White
White Yellow White
White Yellow White
White Yellow White
White Yellow White
White Yellow White
24
White White Orange
White White Orange
White White Orange
White White Orange
White White Orange
White White Orange
25
Second Position of Codon
T
T
C
A
G
TTT Phe [F]
TTC Phe [F]
TTA Leu [L]
TTG Leu [L]
TCT Ser [S]
TCC Ser [S]
TCA Ser [S]
TCG Ser [S]
TAT Tyr [Y]
TAC Tyr [Y]
TAA Ter [end]
TAG Ter [end]
TGT Cys [C]
TGC Cys [C]
TGA Ter [end]
TGG Trp [W]
CCT Pro [P]
CCC Pro [P]
CCA Pro [P]
CCG Pro [P]
CAT His [H]
CAC His [H]
CAA Gln [Q]
CAG Gln [Q]
CGT Arg [R]
CGC Arg [R]
CGA Arg [R]
CGG Arg [R]
ACT Thr [T]
ACC Thr [T]
ACA Thr [T]
ACG Thr [T]
AAT Asn [N]
AAC Asn [N]
AAA Lys [K]
AAG Lys [K]
AGT Ser [S]
AGC Ser [S]
AGA Arg [R]
AGG Arg [R]
GCT Ala [A] GAT Asp [D]
GCC Ala [A] GAC Asp [D]
GCA Ala [A] GAA Glu [E]
GCG Ala [A] GAG Glu [E]
GGT Gly [G]
GGC Gly [G]
GGA Gly [G]
GGG Gly [G]
F
i
CTT Leu [L]
r
s
CTC Leu [L]
t C CTA Leu [L]
CTG Leu [L]
P
o
ATT Ile [I]
s
i A ATC Ile [I]
ATA Ile [I]
t
i
ATG Met [M]
o
GTT Val [V]
n
GTC Val [V]
G
GTA Val [V]
GTG Val [V]
T
C
A
G T
h
T i
C r
A d
G P
T o
s
C i
A t
G i
o
T n
C
A
G
26
Materials:
 Permanent
 Scissors
 Copies of DNA
 Copies of DNA sequencing
 Copies DNA codes for proteins
 Blender
 Ice bucket
 Measuring cup
 1/8 Measuring spoon
 Strainer
 Clean empty milk jug (for water)
 Copies of gel electrophoresis results
 Gel for electrophoresis model
 Copies of gel photographs
 DNA models (optional)

Consumable
 4 red licorice sticks
 2 black licorice stick
 color mini marshmallows
 white mini marshmallows
 wax paper
 toothpicks
 Color paper for copies of proteins
 Copies of DNA sequence
 Copies of restriction enzymes
 Cups
 Centrifuge tubes
 Isopropyl alcohol (at least 95%)
 Ice
 Salt
 Liquid dish soap
 Unseasoned meat tenderizer
 Dried peas
 Sterile swabs
 Glue sticks
 Masking tape or small labels
 Permanent markers – fine point
 Copies of Amino Acid circles
27
-
Gel Electrophoresis Chamber
DNA starts here
DNA starts here
DNA starts here
DNA starts here
50
45
40
35
30
25
20
15
10
5
+
28
29
You and your partner select different sequences below.
 DNA Sequence 1: T A C G T A T G A A A C
-or
DNA Sequence 2: T G G T T T A G A A T T
DNA:
o
o
Adenine (A) binds with Thymine (T)
Guanine (G) binds with Cytosine (C).
o
o
Adenine (A) binds with Uracil (U)
Guanine (G) binds with Cytosine (C).
RNA:
Marshmallow Table
Nucleic Base
Adenine
Thymine
Guanine
Cytosine
Uracil
AMINO ACID KEY
Code
AAA
Amino Acid
Red
Color of Marshmallow
Green
Pink
Orange
Yellow
White
ACC
ACU
AUG
CAU
UAA
UCU
UUG
Orange
Orange
Yellow
(start)
Green
Blue
(stop)
Purple
White
30
Suspect 1
T A T G C C A T T A C G A T A T C A C G T A 1

............................................................................................................
G G G A T A T C C G A T A T C A T T A G A T 2

............................................................................................................
T C T T C G T T A G C C C T A G G A T T A C 3

............................................................................................................
C T T A T T A C C T G A G G A T A T C T A G 4

-------------------------------------------------------------------------------Suspect 2
T A T G C C A T T A C G A G A T T A C G T A 9

............................................................................................................
G A T A T C T A C C A T A C G A T A T C A T 10

............................................................................................................
A A T T C G T T A G A T A T C G G A T T A C 11

............................................................................................................
C T T A T T A C C T G A T A T C A G G T A G 12
31
Suspect 3
T A T G A T A T C A C G A T A T C A C G T A 5

............................................................................................................
G G G A C C T A C C A T A C G A T T A G A T 6

............................................................................................................
A A T T C G T T A G A T A T C G G A T T A C 7

............................................................................................................
C T T A T T A C C T G A T A T C A G G T A G 8

-------------------------------------------------------------------------------Crime Scene
T A T G C C A T T A C G A G A T T A C G T A 13

............................................................................................................
G A T A T C T A C C A T A C G A T A T C A T 14

............................................................................................................
A A T T C G T T A G A T A T C G G A T T A C 15

............................................................................................................
C T T A T T A C C T G A T A T C A G G T A G 16
32
 EcoRV
 EcoRV
 EcoRV
EcoRV
G A T A T C G A T A T C G A T A T C G A T A T C
 EcoRV
EcoRV
 EcoRV
 EcoRV
G A T A T C G A T A T C G A T A T C G A T A T C
 EcoRV
 EcoRV
 EcoRV
EcoRV
G A T A T C G A T A T C G A T A T C G A T A T C
 EcoRV
 EcoRV
 EcoRV
EcoRV
G A T A T C G A T A T C G A T A T C G A T A T C
 EcoRV
 EcoRV
 EcoRV
EcoRV
G A T A T C G A T A T C G A T A T C G A T A T C
EcoRV
 EcoRV
 EcoRV
 EcoRV
G A T A T C G A T A T C G A T A T C G A T A T C
33
34
Materials:
 Permanent
 Scissors (in teacher kit)
 Copies of DNA
 Copies of paper Electrophoresis
Carriage
 Copies of DNA sequencing
 Copies DNA codes for proteins
 Copies of crime scene gels
 Clean container (for water)
 Copies of color amino acids
 Small Ice Chest

Consumable
 24 red licorice sticks (or same color
twizzle sticks)
 12 black licorice stick (or different
color twizzle sticks)
 color mini marshmallows
 white mini marshmallows
 wax paper
 toothpicks
 Copies of DNA sequence
 Copies of restriction enzymes
 3 oz Cups
 Centrifuge tubes
 Isopropyl alcohol (at least 95%)
 Ice
 Salt
 Liquid dish soap
 Unseasoned meat tenderizer
 Sterile swabs or craft sticks
 Glue sticks
 Masking tape or small labels
 Permanent markers – fine point )
35
36