Download VE #15

VE #15
Modeling DNA and Protein Synthesis
Integrated Science 4
3/15
Per.
Name:
 Background
Genes are the functional units of DNA. Genes are expressed by the proteins that they dictate (code
for). DNA is found in the nucleus, but proteins are synthesized at the ribosomes in the cytoplasm.
Therefore, a molecule is needed to carry the DNA code from the nucleus to the ribosomes. This messenger
molecule is appropriately called messenger RNA (mRNA).
Protein synthesis involves two major steps, each with its own kind of RNA. The first step, which
takes place in the nucleus, is called transcription. In this step, a messenger RNA (mRNA) molecule will be
produced by pairing mRNA nucleotides with a half “ladder” of a DNA molecule. This mRNA will then
leave the nucleus and go to a ribosome in the cytoplasm. The ribosome is also made up of a form of RNA,
called ribosomal RNA (rRNA). The second step, which takes place in the ribosomes, is called translation.
During translation, the mRNA will attract yet 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
Amount
Model Description
Cytosine (C)
3
blue tubes
3
green tubes
Nitrogen Thymine (T)
bases
Adenine (A)
3
orange tubes
Guanine (G)
3
yellow tubes
Phosphates
12
white tubes
Hydrogen bonds
6
white rods
Deoxyribose sugars
12
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) with guanine
(yellow)
using
Figure
1
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:
___ ___ ___ ___ ___ ___
___ ___ ___ ___ ___ ___
Part 2. 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)
Model Description
Molecule
Model Diagram
blue tubes
lavender tubes
Ribosomes (1)**
orange tubes
yellow tubes
Phosphates (6)**
white tubes
Hydrogen bonds (12)**
white rods
Ribose sugars (6)***
purple pentagons
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.
(DNA A-T; RNA A-U).
** The numbers in parentheses indicate the quantity of molecules needed for this simulation, if no quantity is given,
then it varies for that molecule.
***Ribose sugar is similar to deoxyribose and is found in all forms of RNA. Deoxyribose has one less oxygen atom.
2. Build a 6 rung DNA “ladder” (this was completed in Part 1). 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 Figure 4
sugar (purple pentagon) and one of four bases (A, U, G or C). See 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.
7
Figure 5
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.
Part 3. 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 peptide bonds (grey tubes) between adjoining amino acids.
See Figure 9.
Figure 9
8. Disconnect the polypeptide (amino acid chain) from the tRNAs.
This is the end of Translation.
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.
9. Unless otherwise directed, disassemble the model pieces and return each part to its appropriate storage
bag.
 Discussion
Answer the following questions in the space below.
1. In an analogy between a factory and a cell, DNA represents the superintendent, mRNA represents the
blueprint for construction and tRNA represents the assembly line workers. Create another analogy
representing the roles of these macromolecules.
2. What is the source of free amino acids in the cytoplasm?
3. List the following structures by order of size: gene, cell, chromosome, atom, nucleus, nucleotide base
subunit, nucleotides. Draw and label a scaled diagram of each of these structures.
4. What might be the result of a mutation of DNA in which a triplet code such as CAC now says CTC?