Protein Structure
Biology
HS
DNA Mutations
DNA to Proteins
These activities are computer simulations, so having students as close to 1to1 with a computer is ideal. Plan significantly in advance of this activity to ensure you have access to computers (state testing requisitions, other teacher use, etc).
Laptops that require power cords should have power strips placed in such a way that walkways are kept clear.
The controls for the simulations are not always intuitive to new users. However, they always have very descriptive assistance provided in the text preceding the simulations. Encourage frustrated students to review the written instructions before attempting to interact with the model further.
There is no equipment required beyond a computer with sufficient power to run the simulations.
Both activities fit best into a regular class period of 45 or 50 minutes when considering time for giving students instructions and technology setup and teardown. The two activities would not fit well together into a block period, and if they are to be used this way it is recommended to plan an intermediate activity to put between them that is more kinesthetic.
The DNA Mutations activity focuses on the discovery question: What are the different types of mutations? The Protein Structure activity focuses on the discovery question: What role does DNA play in protein structures? There is a popular idea in biology that has been termed "The Central Dogma". The Central Dogma states that information is stored in DNA by its sequence of nucleotides. It also states that same information is expressed by being translated to a sequence of amino acids comprising a protein dictated by the original sequence of nucleotides. This general belief regarding the behavior of biological information directs a wide variety of thinking across the field of biology.
The primary misconception held by students when learning about the flow of information in a cell is that the process can be be overly simplified. While the basic flow of information can be grasped fairly quickly, the details of how information is moved become important in order to begin to explore the great many intricacies and exceptions in the process. At many points in the unit teachers do many things to help students grasp new material, but be wary of over simplifying the process. Push your students to wrestle with details they may rather overlook.
How is a molecule of DNA created out of individual atoms?
Bonds are broken and reformed between atoms of other molecules to produce a specific structure, the double helix. This would be a great time to use manipulatives or atomic models.
If you had to communicate English words (26 letter alphabet) using only our numbers (10 digits), how would you do it?
Use multiple digits to represent single letters.
What if you had to use our 26 letters to communicate numbers (10 digits) and every letter had to stand for something?
Make some of the letter duplicate, with multiple letters meaning the same number.
What part of the DNA can change along the strand?
The nitrogen bases can be different, with each base having any of the four possibilities [A, C, T, G].
What are the steps required to express the information contained in a DNA molecule?
DNA must be used to create messenger RNA, mRNA. mRNA then leaves the nucleus and is used to create an amino acid chain, a protein. The first process is called transcription and the second process is called translation.
What happens when a cell experiences a mutation?
A mutation is when any change occurs to the DNA sequence. Mutations can cause a cell to die, to become less able to survive, can have no effect at all, or in very rare cases can make the cell better able to survive.
What kind of mutation has the greatest effect on a cell's DNA?
Choices can vary, but correct answers should contain the idea that any mutation that causes a frame-shift mutation has a catastrophic effect on the sequence in question.
There are three molecules closely related to the flow of information in a cell. What are those three molecules, and what role does each one fill in the cell?
DNA stores the cell's information, RNA moves the cell's information, and proteins express the cell's information.
Organisms big and small achieve the highly diverse structures and behaviors seen in nature through their highly varied protein structures. Humans use 21 amino acids to synthesize proteins, and that number fluctuates across the tree of life surprisingly little. Within those amino acids there are carbon rings, polar groups and nonpolar groups, acidic and basic groups, and even one with only an H for its side chain! The highly varied chemical properties of the amino acids themselves allows for a rich tapestry of proteins that can be built from the limitless combinations possible in any given amino acid chain.
In order to create useful chains of amino acids, cells store information for their proteins in the highly stable DNA molecules within their nucleus. DNA does not degrade over time the way proteins do, which allows them to pass the information for their proteins on to future generations. There is also an intermediate step in which DNA is used to create RNA before the protein is made. This allows a greater number of opportunities for regulation of the gene's expression, and the system is also most likely a relic from the first ancient cells that used RNA exclusively before the rise in use of DNA for storage and proteins for enzymatic activity.
Do you think brachydactyly is an example of a genetic mutation? Explain your reasoning.
Yes and no... the condition is the result of a mutation. The condition itself is a result of an allele, either inherited or spontaneously arisen from a mutation.
Hydrophilic amino acids are attracted to water. Hydrophobic amino acids are not attracted to water, and tend to clump together. In the substitution model, was the synthesized amino acid hydrophobic?
Will vary. Use the color coded model to determine the result of each individual's mutation.
How can an insertion or deletion mutation make a protein much shorter than it should be?
Any mutation that creates a stop codon will cause the protein to be truncated at the spot of the mutation, possibly removing hundreds or thousands of amino acids from the downstream chain.
How did you create a silent mutation? Explain, giving the code for the triplet where you made your substitution, before and after the mutation.
Silent mutations are caused by exchanging a nitrogen base for a different base that creates a codon for the same amino acid as the original. This mutation is almost always in the third base of a triplet.
How did you make an insertion or deletion mutation that did not cause a frame-shift?
any insertion or deletion that contains a number of bases that is a multiple of three will not cause a frame-shift.
How can a mutation be neutral?
Any mutation that is silent is neutral, by definition. However, other mutations that don't cause any structural or chemical changes to the protein are also neutral. One example may be a mutation that changes the amino acid to one that is chemically similar and in a location that does not play a big role in the protein's function.
Which types of mutation, among those you created in this activity, are more likely to be lethal? Why?
Frame-shift mutations are much more likely to be lethal because they result in total destruction of all information downstream of the mutation.
What are the different types of mutations?
Insertion - addition of bases, deletion - removal of bases, substitution - change of one or more bases to different bases, duplication - insertion of bases with identical sequence to neighboring sequences, translocation - deletion of a sequence of DNA and an associated insertion of the same DNA sequence elsewhere in the genome, and inversion - changing a DNA sequence to its mirror opposite.
How can a mutation in a cell's DNA affect its growth?
A mutation can have any possible effect, positive or negative, depending on how it changes the efficiency of the protein being coded by that sequence.
What diseases would you want to search for a cure for if you were a cell biologist?
will vary.
Why do mutations that create a stop codon have a bigger effect on the protein than other mutations?
Creating a stop codon removes all downstream information, whereas other point mutations have a localized effect only on the codons they directly impact.
There are millions of cells' worth of DNA in this tube. What do you think DNA looks like under a microscope?
will vary.
Describe the nucleotide pairings that you see.
will vary.
List two ways in which the RNA strand in the model above is different than DNA strand from which it was copied (the template strand). If six bases on the template strand of DNA are AGTAAC, what are the six bases on the complementary section of the RNA?
U is used instead of T, it is single stranded instead of double. RNA sequence is UCAUUG
What happens in translation? Compare the sequence and shape of both proteins that are formed.
will vary. Most notably is movement by 3 bases instead of one, and production of amino acid sequence instead of nucleic acid sequence.
Which one of the following is the place where genetic information is stored in the cell?
information is stored in the "strands of DNA"
How many nucleotides would you need to code for a protein with a sequence of 24 amino acid?
72. 24 x 3 bases per codon for each amino acid = 72
What is the connection between the DNA sequence of a gene and the amino acid sequence of the protein which is produced from that gene?
The DNA sequence dictates the RNA sequence, which dictates the amino acids used to build the protein. As a result, the DNA sequence controls the amino acid sequence produced.
What role does DNA play in protein structures?
DNA holds the information that dictates the resulting protein's structure.
Why do cell biologists work to discover the genomes of living things?
If we know the genome of a living thing, we can better understand the structure of that thing's proteins.
Would you want to be a cell biologist? Why or why not?
will vary.
If you change the code for Leucine, in the second codon, from UUG to AAA, what will be the end result?
Leucine will not be used in that spot on the amino acid chain. Instead Lycine will be used, which is hydrophilic instead of hydrophobic.
The Central Dogma is only the beginning of how information flows in living systems. There are many exceptions, and students can investigate some of the less complex examples.
Prions are proteins that interact with other proteins to change their function. Prions cause some well known diseases, such as Mad Cow Disease. How is information transferred in prion function?
Diseased proteins transfer information to healthy proteins, which creates more diseased proteins. Protein &rarrow; Protein)
Some viruses transfer information in unconventional ways in order to reproduce. HIV uses a genome of RNA. What is the flow of information to create an HIV protein?
HIV creates DNA from RNA, which then creates more RNA, which is then used to create protein.