Download Modeling DNA Replication and Protein Synthesis

Modeling DNA Replication and Protein Synthesis
Integrated Science 4 Honors
Name:
Per.
Background
Genes are functional units of DNA. They express themselves by the proteins they dictate. DNA is
found in the nucleus, but proteins are synthesized at the ribosomes in the cytoplasm. Thus a messenger
molecule is needed to carry the DNA code. This messenger molecule is called messenger RNA (mRNA).
Protein synthesis involves two major steps, each with its own kind of RNA. In the first step, called
transcription, a messenger RNA (mRNA) molecule will be produced by pairing mRNA nucleotides with a
half “ladder” of a DNA molecule. This mRNA will leave the nucleus and go to a ribosome in the
cytoplasm. The ribosome is made up of a form of RNA as well, called ribosomal RNA (rRNA). In the
second step, called translation, the mRNA will attract another form of RNA called transfer RNA (tRNA).
These tRNAs will bring in and place amino acids in the proper sequence to produce the specific protein as
ordered by the gene that was transcribed.
The purpose of this activity is to review the molecular make-up of DNA, RNA and protein synthesis.
Replication of DNA, transcription and translation of RNA are modeled as well.
Procedures
Part 1. DNA Model
1. Working in pairs, you will construct a 6 rung DNA model using the following components:
Molecule
Cytosine (C)
Nitrogen Thymine (T)
bases
Adenine (A)
Guanine (G)
Phosphates
Hydrogen bonds
Deoxyribose sugars
Amount
3
3
3
3
12
6
12
Model Description
blue tubes
green tubes
orange tubes
yellow tubes
white tubes
white rods
black pentagons
2. Build 12 nucleotides: 3 each of cytosine (C), Guanine (G), Adenine (A) and
Thymine (T). A nucleotide of DNA consists of a phosphate, a deoxyribose
sugar and one of the four bases (A, T, C or G). See Figure 1.
3. Use these nucleotide units to construct a 6 rung ladder of DNA. Match
nucleotides of adenine (orange) with thymine (green) and cytosine (blue)
Figure 1
with guanine (yellow) using white rods (hydrogen bonds). You may choose the sequence of bases, but
have at least one of each color on both sides of your ladder. Bond the phosphate of each nucleotide to
the sugar unit of the neighboring nucleotide. See Figures 2 and 3.
Figure 2
Figure 3
4. Orient your DNA ladder to resemble Figure 3. Record the sets of complimentary base pairs from left to
right:
___ ___ ___ ___ ___ ___
___ ___ ___ ___ ___ ___
5. Have your teacher initial that your DNA model is built correctly here:
.
6. Draw and label the 6 rung DNA model you have just created in the section labeled Application –
Modeling DNA Structure on the activity titled DNA Structure and Replication.
Part 2. DNA Replication
1. Build 12 additional nucleotides of DNA (3 each of C, G, A and T), but do not make a second ladder.
2. Unzip the DNA ladder by breaking the weak hydrogen bonds that hold the two DNA strands together.
3. As the DNA ladder is unzipped, bring in the new nucleotides (built in step 1) complementary to the
“template” ones on the half ladders. You now have two identical models, one half of each model is
original and one half is newly formed. Recall, this process occurs with DNA in all cell chromosomes
prior to mitosis and meiosis so that new cells being formed will have a copy of each chromosome.
4. Have your teacher initial that you have modeled DNA replication correctly here:
. Unless
otherwise directed, disassemble the model pieces and return each part to its appropriate storage bag.
Part 3. Transcription
1. Working in pairs, you will model protein synthesis using the following components:
Molecule
Cytosine (C)
Nitrogen Uracil (U)
bases
Adenine (A)
Guanine (G)
Phosphates (6)*
Model Description
blue tubes
lavender tubes
orange tubes
yellow tubes
white tubes
Hydrogen bonds (12)*
white rods
Ribose sugars (6)*
purple pentagons
Molecule
Model Diagram
Ribosomes (1)*
tRNA (2)*
Amino Acids (2)*
Peptide bonds (2)*
gray tubes
*Note: Uracil is a molecule similar to thymine and substitutes for it in RNA. Uracil will always bond to adenine.
Ribose sugar is similar to deoxyribose and is found in all forms of RNA. Deoxyribose has one less oxygen atom. The
numbers in parentheses indicate the quantity of molecules needed for protein synthesis, if no quantity is given, then it
varies for that molecule
2. Build a 6 rung DNA “ladder” (this may be completed for you). Using your desk top to stimulate a cell,
place the DNA on a portion of the desk top chosen as the nucleus and marked with chalk or a piece of
tape; the rest of your desk can be the cytoplasm of the cell. Place the ribosome, transfer RNAs and
amino acids in the cytoplasm.
3. Orient your DNA ladder to resemble Figure 3. The top half of the DNA ladder (no phosphate on the left,
phosphate on the right) will be your “template” for transcription.
4. Unzip the DNA ladder by breaking the weak hydrogen bonds that hold the two
DNA strands together.
5. In the nucleus of the cell you created, build 6 mRNA nucleotides that are
complementary to the “template” strand of DNA. (Remember that if DNA has
adenine, it must match with uracil in RNA). A nucleotide of RNA consists of a
phosphate, a ribose sugar (purple pentagon) and one of four bases (A, U, G or C). See Figure 4.
Figure 4
6. Bond each mRNA nucleotide with the complementary base of the DNA and to each adjoining mRNA
nucleotide by attaching the sugar of one to the phosphate of the next in line. See Figure 5.
Figure 5
7
7. Unzip the newly formed mRNA molecule by breaking the weak hydrogen bonds connecting it to the
DNA template strand. (Note: The DNA can zip back together or help form a new mRNA).
8. Take the “free” mRNA molecule from the nucleus and place on the ribosome in the cytoplasm. This will
be the site of protein synthesis. The process of Transcription is now complete.
9. Have your teacher initial that you have modeled Transcription correctly here:
.
Part 4. Translation
1. The sequence of bases of mRNA created in Part 3 has the message for the construction of a specific
protein. This code works in units of three nucleotides called “triplet” codons. A triplet codon of mRNA
will attract another form of RNA called transfer RNA (tRNA), a small molecule which has a double
attraction to both a triplet codon of mRNA and to an amino acid. The tRNAs act as a construction
worker, bringing the amino acids into proper sequence at the mRNA in order to construct a protein.
The 20 basic amino acids are found in cytoplasm after being digested and absorbed from foods
containing proteins.
2. Record the sequence of nucleotide bases along your mRNA molecule: ___
___ ___ ___ ___
___.
3. Construct two tRNA molecules by adding 3 nucleotide bases to each tRNA. Recall that each tRNA
anticodon sequence must be complementary to the mRNA codon it pairs up with.
Ex.
Triplet of bases on mRNA – AGC (codon)
Triplet of bases on tRNA – UCG (anticodon)
4. Gather two amino acids. Notice the shape in the middle
of each piece is unique. Attach an amino acid to each
tRNA by matching up complementary shapes. These
shapes represent different R-groups found on amino
acids. See Figures 6 and 7.
Figure 6
5. Place the mRNA on the model ribosome, the site of protein
synthesis. Act as the ribosome and read the first mRNA
codon. Bring the complimentary tRNA-amino acid complex
to the codon of mRNA. Attach anti-codon to codon with
hydrogen bonds. See Figure 8.
Figure 7
6. Shift the ribosome and read the second mRNA codon.
Bring the complimentary tRNA-amino acid complex to the codon of mRNA.
Attach anti-codon to codon with hydrogen bonds.
Figure 8
7. Attach covalent (peptide) bonds (grey tubes) between adjoining
amino acids. These peptide bonds are formed through a series of
dehydration synthesis. See Figure 9.
Figure 9
8. Disconnect the polypeptide (amino acid chain) from the tRNAs.
This is the end of Translation.
9. Have your teacher initial that you have modeled Translation correctly here:
.
Note: When actual proteins are being created, the polypeptide chain will then coil, twist or fold and even
may link with other chains. The result is a protein built to the exact specifications of the DNA code. The
tRNAs are then disconnected from the mRNA. Both are now available to be used again in the cytoplasm.
10. Unless otherwise directed, disassemble the model pieces and return each part to its appropriate storage
bag.
Analysis
Consider the analogy to the process of protein synthesis:
• You need a vital piece of evidence for a large report.
• The information is found in a valuable set of encyclopedias found in the Redwood library. The
encyclopedias are written in Mandarin.
• The library will not let you check the Mandarin encyclopedias out (they cost too much), but you
cannot write your report at the library.
• Therefore, you must locate the correct volume of the encyclopedia and make a photocopy of the
relevant pages.
• You will take the copy of the evidence/information to your home where you will write the report.
• Before you can use the photocopy, you must give them to someone who understands both Mandarin
and English and will produce an English version of the information which you can actually use.
• You may now incorporate the English version of the information into your final report.
1. Identify the following as they appear in this analogy: nucleus; chromosome; ribosome; protein;
polypeptide; translation; transcription; DNA; mRNA; tRNA.
2. List and draw/sketch, ordered by size, the following: gene, cell, chromosome, atom, nucleus,
nucleotide base subunit, nucleotides.
3. Identify any (5) human proteins and the cells that produce those proteins. Select (1) of those proteins
and discuss the possible outcomes to a mutation in the gene/DNA sequence for that protein.