K’Nex Modeling of DNA Lab
Recall that the nucleus is a small spherical, dense body in a cell. It is often called the
"control center" because it controls all the activities of the cell including when a cell divides
into two, and heredity. Chromosomes are microscopic, threadlike strands composed of the
chemical DNA (short for deoxyribonucleic acid). In simple terms, DNA holds the instructions
for making proteins within a cell. In fact, the only things that DNA is capable of producing is
proteins. These proteins in turn, form the structural units of cells and control all chemical
processes within the cell. Think of proteins as the building blocks and work horses for an
organism. How you look is largely determined by the proteins that are made. The proteins that
are made are determined by the sequence of DNA in the nucleus. In short, DNA makes
proteins, and proteins run all the processes in your cells.
DNA is composed of genes, which are segments of DNA that codes for a particular
protein which in turn codes for a trait. Hence you hear it commonly referred to as the gene for
baldness or the gene for blue eyes. There are an estimated 20,000 to 25,000 genes in the
human genome. That’s only 200 to 250 more than our close relative the chimpanzee. Yet those
200 to 250 genes make a big difference.
DNA is a polymer of a nucleic acid because it was first found in the nucleus. We now
know that DNA is also found in other organelles such as the mitochrondria and chloroplasts,
though it is the DNA in the nucleus that actually controls the cell's workings.
In 1953, James Watson and Francis Crick figured out the structure of DNA, with the
help of Rosalind Franklin, Maurice Wilkens and Erwin Chargraff. The shape of DNA is a double
stranded helix, which is like a twisted ladder. The two strands run antiparallel to one another,
or in opposite directions. The sides
of the ladder are made of
alternating deoxyribose sugar and
phosphate molecules.
The rungs of the ladder are
pairs of 4 types of nitrogen bases.
The bases are known by their coded
letters A, C, G, T. These bases
always bond in a certain way.
Adenine will only bond to thymine.
Guanine will only bond with cytosine.
This is known as the "Base-Pair
Rule". The bases can occur in any
order along a strand of DNA. In
fact, the order of these bases will
determine the type of protein that
is made. For instance the gene ATGCACATA would code for a different
protein than the gene AATTACGGA. Our example is oversimplified. In
reality, a strand of DNA contains millions of bases.
Note: looking at the picture on the previous page you will see that the bases
attach to the sugars and not the phosphates.
DNA is actually made of smaller repeating monomers called nucleotides. Each
nucleotide consists of three molecules: a sugar (deoxyribose), a phosphate
which links the sugars together, and then one of the four bases. Two of the
bases are classified as purines - adenine and guanine, and the other two
bases are classified as pyrimidines - thymine and cytosine. Note that the
pyrimidines are single ringed and the purines are double ringed.
Nucleotide
Pyrimidine
s
Purine
The two sides of the DNA ladder are held together loosely by
hydrogen bonds. The DNA can actually "unzip" when it needs to replicate - or make a copy of
itself. DNA needs to copy itself when a cell divides, so that the new cells each contain a copy of
the DNA. Without these instructions, the new cells wouldn't have the correct information.
Every cell in your body has the same "blueprint", or the same DNA. Just as the blueprints
of a house tell the builders how to construct a house, the DNA "blueprint" tells the cell how to
build the organism. Yet, how can a heart be so different from a brain if all the cells contain
the same instructions? Although much work remains in genetics, it has become apparent that a
cell has the ability to turn off most genes and only work with the genes necessary to do a job.
We also know that a lot of DNA apparently is nonsense and codes for nothing. These regions of
DNA that do not code for proteins are called "introns", or sometimes "junk DNA". The sections
of DNA that do actually code from proteins are called "exons".
PRELAB QUESTIONS: Please use rubric writing style and cite your source in your answer.
(Except for number 9)
1. What is the function of DNA?
2. What does DNA code for in our cells?
3. What is a gene?
4. Besides the nucleus, name two other organelles that contain DNA?
5. What two scientists are credited for discovering the structure of DNA?
6. What are the two sides of the DNA ladder made of?
7. What are the “rungs” of the DNA ladder made up of?
8. What are the three components of a nucleotide?
9. Write the complementary sequence to the following DNA sequence: The first three have
been written for you.
Sugar/Phosphate sides
T A T T G C A G A T A A C T G
A T A
Nitrogen Bases
PROCEDURE:
1. Using the instructions in the K’Nex manual, as a group, build several nucleotides. Divide up
the work so that a TOTAL OF 24 NUCLEOTIDES ARE MADE: 6 Adenines, 6
Guanines, 6 Cytosines, and 6 Thymines. DON’T JUST COPY WHAT THE MODEL
LOOKS LIKE IN THE MANUAL; FOLLOW THIS LAB PLEASE!
2. Attach the nucleotides to one another so that the end of the phosphate group in one
nucleotide connects to the deoxyribose sugar of the next one.
3. Make one strand of nucleotides using a RANDOM sequence of nucleotides. DON’T copy the
manual’s DNA sequence.
4. After you’ve made one random DNA sequence, follow the rules of DNA base-pairing, and the
instructions in the Manual (pages 3-5) in order to build the complimentary strand. MAKE SURE
YOUR STRANDS RUN ANTIPARALLEL to one another.
5. Before you twist your strand into a helix, read post-lab question 5 below.
6. Use the manual to hydrogen bond the DNA strands together, add red rods, create the base,
and twist the double-stranded DNA into a helix (as shown on pages 6-7 of manual). FOUR
BASES MUST BE USED PER RED ROD. YOU ONLY NEED THREE RED RODS IN THE CENTER.
7. Once you have constructed your DNA model, write down the sequence of bases in one of the
strand.
8. Compare your sequence to the other groups in the classroom. Are any of them the same?
Why or why not?
POST LAB QUESTIONS: Please follow your standard writing rubric for full points. If it is
appropriate to cite a source, you must do so to get full credit.
1. Which pieces represented the deoxyribose sugar?
2. Which pieces represented the phosphate group?
3. Which color was each nitrogenous base represented with?
4. Why are the adenine and thymine bases joined with an orange connector, while the
cytosine and guanine bases were joined together by a brown connector?
5. Compare the stability of the flat DNA model (before you twisted it) to the helical (spiral)
DNA model that you created. Which one is more stable? (Hint: if you can’t figure it out, think
about if a sheet of paper is more stable than a sheet that is twisted into a cord).
6. Based on your answer to number 5, why do you think the DNA is shaped like a helix in our
cells (how is it helpful)?
7. Compare the sequence you made to the sequence of other groups’ DNA models in the room.
Are any of them the same? How does this relate to a comparison between your DNA, and
others DNA in the room? Does anyone in the room have the exact same DNA? Explain.
Grading Rubric:
1. DNA Model (10 pts) Part 1 of Project Grade
A. Model contains 12 correctly paired complementary bases _____ / 2 pts
B. Deoxyribose and phosphate group connected correctly _____ /2 pts
C. Helix is shown accurately (four bases per red rod)
_____ /2 pts
D. DNA strands were assembled in ANTIPARALLEL fashion _____ /2 pts
E. Stand was created correctly, and DNA molecule sits properly ____ /2 pts
2. Pre-Lab questions and questions within the procedures (10 pts) Part 2 of Project Grade
3. Post – Lab Questions ( 14 pts) Test Grade
A. all questions answered accurately and according to rubric______ / 14 pts