Download DNA Kit Lab

DNA Kit Lab
Background Information:
One of the most important and exciting scientific discoveries of recent years is the discovery of
deoxyribonucleic acid (DNA), a chemical which holds the secret of life itself. For many years, biologists
studying heredity had believed that hereditary information was stored in proteins. Then in 1953 two scientists,
James Watson and Francis Crick, produced a model of DNA which detailed how hereditary information could
be stored in this molecule. Further testing showed that the Watson-Crick model was indeed correct. DNA, and
not proteins, proved to carry the genetic code for life.
James Watson and Francis Crick
Purpose:
At the end of this lab you will be able to construct a two-dimensional model of DNA and understand the
processes of replication, transcription, and translation.
Procedure:
This lab has been designed to follow a series of sequential steps. After each step, a series of questions
will appear. In order to answer the questions correctly, each step of the lab must be carried out before attempting
to answer the questions. All lab instructions are written in italics.
DNA and RNA Kit Piece Identification
1. Remove the pieces of the model from the box and place them in front of you letter side up. These pieces
are representatives of actual chemicals found in the DNA molecule. The letters stamped on each piece
are merely identifiers. (Therefore, the piece labeled “A” is simply piece “A”. The “A” stamped on the
piece does not mean that this particular piece is adenine.) You should have the following number of
pieces in your kit.
Letter
A
B
C
D
E
F
G
H
J
OH
Amino Acid
No. of Pieces
24
12
24
6
6
6
6
4
6
4
4
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Once you have sorted the pieces, return the H, OH, and amino acid pieces to the box. These will be used later in
the lab.
2. Line-up one of each of the following pieces in front of you: A, B, C, D, E, F, G, and J. Place all the extra
pieces off to the side. These pieces represent DNA and RNA chemicals.
3. Using only these 8 pieces from step #2, try to bond them together in pairs of two. Some of the pieces
will pair together very tightly (2 pieces interlocked tightly so that when 1 piece is picked up off the
table, the other piece travels with it). This type of pairing represents a covalent bond. Some of the pieces
will pair together very loosely (2 pieces interlocked loosely so that when 1 piece is picked up off the
table, the other piece remains on the table). This represents a hydrogen bond.
a. Identify the type of bond made by the pairing of the following pieces?
i.
ii.
iii.
iv.
Put
Pieces B and C = ______________
Answers
Pieces A and G = ______________
Pieces G and F = ______________
On Answer
Pieces E and J = _______________
Sheet
4. The chemicals that make up DNA and RNA are very similar. Study the table below to identify the main
building blocks of these two molecules and then answer some questions.
Sugars
Phosphate
Bases
DNA
Deoxyribose
Phosphate
Adenine
Guanine
Cytosine
Thymine
RNA
Ribose
Phosphate
Adenine
Guanine
Cytosine
Uracil
a. How many kinds (types) of sugar are in DNA? In RNA?
b. How many different kinds (types) of bases are there between DNA and RNA?
c. How many different kinds (types) of phosphate are there between DNA and RNA?
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5. It is now time to figure out which chemical each piece actually represents. Arrange the pieces into three
piles based upon their similar characteristics. You should have one pile of two pieces, one pile of five
pieces, and one pile with only one piece in it. Using the chart from step #4, you should already have
some idea as to what each of the pieces might actually be. Use the following clues to help you, figure out
the chemical that each piece represents and then fill in the following chart.
Clues
Piece A is Deoxyribose
Piece D is Uracil
Letter Stamped
on DNA Piece
Actual Chemical
Name
A
B
C
D
E
F
G
J
Deoxyribose
Is it found in
DNA, RNA, or
Both?
DNA only
Put Answers On Answer Sheet
Uracil
RNA only
Put
Answers
On Answer Sheet
Constructing the DNA Molecule
6. Now that you know the actual chemical names that each of the pieces represent, it is time to start
constructing DNA. Start by making a nucleotide. A nucleotide is the combination of three pieces; a
sugar, a phosphate, and a nitrogenous base. Using all four of the DNA nitrogen bases and deoxyribose,
construct 12 nucleotides. Put all pieces B’s and D’s back into the box, these are found only in RNA and
are not a part of DNA. (Hint, some of the nucleotides will be the same because there are only four
different DNA nitrogenous bases)
a. What two chemicals are present in every nucleotide constructed?
b. What is the chemical that can vary in each nucleotide?
7. Next, join the nucleotides together. In a DNA molecule, adenine always bonds with thymine and
cytosine always bonds with guanine. When all 12 of your nucleotides have been combined you will
have constructed a double stranded piece of DNA. When you reach this point, have your teacher come
by and initial that you have completed this step on your answer sheet.
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a. What is the advantage in having hydrogen bonds between the bases of 2 strands of DNA?
b. What is the advantage of having covalent bonds between the sugars and phosphates in a DNA
strand?
c. Would errors be easy to spot in a DNA molecule? Why?
d. Where is the chemical code located in the DNA molecule; in the nitrogenous bases or sugars or
phosphates? Why is this the case?
DNA Replication
8.
Now it is time to replicate your DNA. DNA replication is termed semi-conservative because one half of
each new DNA strand is old and one is newly constructed. In order to observe this semi-conservative
replication process, split apart your DNA molecule at its hydrogen bonds and move these single strands
of DNA to opposite sides of the table. Then following the complementary base pairing rules (A-T and CG) attach new nucleotides to one strand to demonstrate replication. When this step is completed, have
your teacher come by and initial that you have completed this step.
a.
b.
c.
d.
What is meant by the term semi-conservative replication?
Why is semi-conservative replication beneficial to organisms?
What enzyme is needed to ‘unzip’ the 2 strands of DNA?
What enzyme is needed to add nucleotides then bond them together to make a new strand of
DNA?
Transcription (TC)
9. Our DNA molecule has now been successfully replicated. It is now time for the DNA to do some
work for the body. DNA carries the chemical code or ‘blueprints’ to make proteins for the body.
Proteins, which are long chains of amino acids, are the building material and enzymes of our cells. They
carry out the work of the cell and are assembled using ribosomes. These ribosomes are located outside
of the nucleus in the cytoplasm or on the endoplasmic reticulum.
Here is where a problem arises. DNA, which holds the code for making all of the body’s
proteins, cannot leave the nucleus and ribosomes cannot go into the nucleus. This is why the body
employs RNA. Ribonucleic acid (mRNA) acts as a messenger in the cell, getting the DNA code outside
of the nucleus to the ribosome which will build the protein.
Let’s build some mRNA; a process called Transcription (TC). Take one of your strands of DNA
(single stranded) and lay it out in front of you. You will have to dissemble the rest of your DNA strands
in order to use the parts to construct your mRNA molecules. Using the one strand of DNA as a template,
construct a corresponding piece of mRNA. Be aware that the bonding rules for mRNA are slightly
different than in DNA. In mRNA, guanine still bonds with cytosine, but adenine now bonds with uracil
(G-C and A-U). Also, the sugar in mRNA is ribose so it looks slightly different than the DNA sugar.
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a.
b.
c.
d.
e.
f.
g.
How is the sugar in mRNA different than the sugar in DNA?
Why is the body making mRNA in the first place?
What are is the primary function of mRNA in the body?
Transcribe the following DNA code into RNA.
What enzyme is needed to ‘unzip’ DNA?
What enzyme is needed to add RNA nucleotides to the DNA template strand?
What type of bond will temporarily bond the RNA bases to the DNA bases?
DNA: T A C G G A T C G A T T
RNA:
Put Answers on Answer Sheet
10. Take your newly constructed strand of mRNA and detach it from its DNA template. This is mRNA
(messenger RNA) and it is now ready to leave the nucleus of the cell and get the DNA blueprint for
constructing a protein out to a ribosome. Move the mRNA to the middle of your table and push the DNA
strand off to the side. Pretend that the mRNA is attaching to a ribosome just like in the picture below.
We are now ready to begin protein synthesis.
a. Why does the mRNA have to go to a ribosome?
b. What are the complementary base pairing codes for a molecule of mRNA?
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11. Now bond your mRNA strand with a complementary strand of tRNA. This step is called translation and
is responsible for building the proteins (protein synthesis). tRNA (transfer RNA) is a “T” shaped piece
or a cloverleaf of RNA that brings individual amino acids to a ribosome, deposits them, and then leaves
in search of another amino acid. The ribosome knows which tRNA to bring in because it reads the
mRNA strand in groupings of three letters at a time. This is called a codon. Each codon codes for a
specific amino acid carried by the individual tRNA’s. The pictures below show what a tRNA molecule
and the process of translation looks like.
tRNA and Translation
Translation (TL)
12. Finally, to complete the protein synthesis process, it is time to translate (TL) the mRNA into a protein. Take
the amino acid, H, and OH pieces from the box. (Remember, we put them in there back in the beginning of the
lab The H’s stand for hydrogen and the OH’s stand for hydroxide.) Attach the H’s and OH’s to the ends of the
amino acids. Then begin bonding mRNA nucleotides with complementary tRNA’s. (The RNA bonding rules are
still the same A-U and G-C)
Once you have assembled 2 tRNA’s (an anti-codon), to your mRNA strand put an amino acid on top of
the tRNA’s. Then, bond three more tRNA’s and attach a second amino acid. Join the amino acids together by
removing and hydrogen from one and a hydroxide from another. Put these two pieces together to form water.
You have now started making a protein. In the body this process would just continue until the mRNA told the
ribosome to stop with one of the 3 stop codon sequences.
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Codon Chart
a.
b.
c.
d.
e.
How is transcription (TC) different than translation (TL)?
What are the 3 different codons that would stop translation?
What are the functions of protein in the body?
What are the RNA bonding rules between mRNA and tRNA?
In order for a ribosome to ‘translate’ the message from the mRNA into a protein, what 2 ‘languages’
must the ribosome be able to speak?
f. What’s the difference between a codon and an anti-codon?
g. In order for the ribosome to bond 2 amino acids, what must be removed from both ends of an amino
acid? What process is this? (hint: the opposite of Hydrolysis)
h. What is the specific name of the covalent bond that joins 2 amino acids?
i.
DNA: A T G C C G T T T G A G
mRNA:
tRNA:
Amino Acids:
Put
Answers
On Answer
Sheet
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Mutations
13. Mutations are changes in the genetic code. Mutations could have negative or positive effect on an organism
but many times have a neutral effect on the creature. Mutations can occur in somatic cells (body cells) and they
can also occur in germ cells (egg and sperm). A mutation could be analogous to a typographical error in a paper,
depending on which letter of a word was accidentally deleted, inserted or re-typed accidentally. Below is an
example of what could occur in a paper
Original Sentence:
The fat cat ate
Substitution Mutation: The fat bat ate
Deletion Mutation:
The fat ata te
Insertion Mutation:
The fat cat lat e
Suppose an animal needed a certain Enzyme X ( remember that enzymes are proteins) to aid in the breakdown
of Glucose in Cell Respiration. The active site of Enzyme X consists of 3 amino acids,
Lysine…..Phenylalanine…Proline. Using the Codon Chart, determine the possible codons for each of the amino
acids. Then, from the determined codons, determine the possible DNA sequences. Fill in the chart on your
answer sheet.
Proline
OR
OR
OR
OR
OR
OR
Fill In Chart on
Answer Sheet
Phenylalanine
OR
Possible DNA Sequence
Fill In Chart on
Answer Sheet
Lysine
Fill In Chart on
Answer Sheet
Possible Codons
Fill In Chart on
Answer Sheet
Amino Acid
OR
14. Assume this particular animal was subjected to a mutagen such as radiation. The radiation caused a
mutation in the DNA base sequence; the triplet code for the ‘chunk’ of DNA that produces Phenylalanine now
reads CAA instead of AAA.
Amino Acid
Phenylalanine
Possible DNA Sequence After
Mutagen Exposure
CAA
Codon after
Mutagen Exposure
Fill In Chart on
Answer Sheet
a. The DNA code was changed to CAA from AAA after exposure to radiation. What type of mutation is this?
b. List the 3 amino acids that are coded for the active site of Enzyme X after the animal’s exposure to the
mutagen
c. Will the enzyme have the correct conformation to add in the chemical reactions of Cell Respiration?
d. Can this animal extract energy from Glucose now?
e. If this mutation occurred in the DNA strand of the animal’s muscle cell (somatic cell), would it be
hereditary?
f. If this mutation occurred in the DNA strand in the animal’s germ cell (egg or sperm), would it be
hereditary?
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