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Activity Overview:
Key concepts:
The sequence of nucleotides in the DNA serves as a genetic code, dictating the sequence of amino acids in proteins.
Students work with the dynamic model Molecular Workbench: From Genetic Code to Protein Structure. They manipulate a sequence of nucleotides in DNA and explore connections between the genetic code, written as a sequence of nucleotides in DNA, the sequence of amino acids and the shape of a protein.Learning Objectives:
Students will be able to:
Reason how DNA, a linear polymer made of millions of monomers of four different types (adenine, thymine, guanine and cytosine), can store the information about sequence of amino acids in proteins.
Conceptual Prologue
To make new proteins, the living cell uses the genetic code of the DNA, which stores all the information about the sequence of all cell's proteins. The position of each amino acid in the protein chain is coded by three consecutive nucleotides of the DNA, called codons. A codon in the genetic code can be compared with a single letter in our human alphabet. These letters are combined in separate "words" - genes, each "remembering" the sequence of a specific protein.
Only recently have scientists finally proven that cellular DNA carries all information necessary to build all of the cell's proteins (about 70-80,000 in number!). Before a cell divides in two, it makes two exact copies of its DNA, one for each offspring. Then the cell "transcribes" this information by making various proteins, in the amount, and at the time they are needed by the cell. The cell does it by opening for copying (i.e. reading the code) or closing a specific part of the DNA that controls a given protein. There are special proteins that do the "closing-opening" job. Therefore DNA in the cell, together with the regulatory proteins that open or close specific part of if, serve as a kind of command and control center, responding to the cell's needs and to different outside signals brought by hormones or nervous impulses.
The genetic code is translated into a protein sequence with the help of several types of molecular machines. First, DNA gets a signal, for example, from a hormone, that a cell needs a protein. Then the part of the DNA that controls this protein, called a gene, becomes active. Proteins that had been "hiding" the gene now allow the gene to be copied (transcribed) onto a messenger that carries information to the cytoplasm where the protein will be made. Such a copy of a gene is another type of nucleic acid, called messenger RNA (mRNA).
The active gene is copied into mRNA with the help from an enzyme that works as a copying molecular machine. Then mRNA moves from the nucleus to the cytoplasm to work with the protein-assembling machine, called a ribosome.
Following the instructions brought by the mRNA, a ribosome assembles a protein. It works as an assembly line, moving along the mRNA, from codon to codon, requesting just one amino acid at a time from the pool of amino acids in the cell's cytoplasm, according to the codon that was "read" at that moment. Special carriers, called tRNA (transfer RNA), respond to the ribosome's request, adding the necessary part (amino acid) to the protein chain growing on the ribosome's assembly line (Fig. 1). A longer story
Major Science Concepts Coding, DNA Assumed Previous Knowledge: Monomers and polymers, amino acids Time: One 50-minute classes Technical Requirements: There is one model in this activity, which can be launched in one of two ways:
1. From your browser. Click the link below.:Modeling Workbench: From Genetic Code to Protein Structure
http://xeon.concord.org:8080/modeler/webstart/protein/dna1.jnlp2. By going through the Molecular Workbench application on your computer (workbench.jar). Then you should click the following links: Student Pages, Protein Folding, From Genetic Code to Protein Structure
It may take a short while to launch the Molecular Workbench the first time.
Supportive Materials: * Background: From DNA to RNA to Protein [PDF version]
* Amino Acid Chart [PDF version]
* Worksheet: From Genetic Code to Protein Structure Worksheet (Student [PDF version]
* Worksheet: From Genetic Code to Protein Structure Worksheet (Teacher)
Advanced preparation Print or bookmark support materials
Prepare model for access (See above)
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Activity Design and Execution
Investigative Question: How can DNA provide the information for making a specific protein, affect the shape of a protein, and therefore the way a protein works?
Steps
Prologue: Engage your students with the DNA zoom, and, if possible, look at the DNA molecule in the Molecular Viewer. The viewer requires requires Mac OS 10.2 or higher, or PC with graphics acceleration card to go at appropriate speed.
1. From DNA to RNA to Protein. Distribute the reading From DNA to RNA to Protein either for homework the night before this class or for students to read in class. Then show students or have students run this DNA animation. (This may work better with Internet Explorer.) After students have completed both, review the information flow process from DNA to Protein with the students.
2. A Codon Exercise. How many possible combinations are there? Have students figure out how many different three-letter "words", such as AAA or ATA etc. can be made from four letters A, T, C and G. To start, you might help them discover for themselves that there are 16 possible "words" beginning with A. The same must be true for words beginning with G, T, and C, for a total of 16+16+16+16 or 64 different words. More
3. Exploring the Role of DNA and Protein Structure. Distribute the From Genetic Code to Protein Structure Worksheet (Student).The worksheets include both instructions for how to use the model, and model-based activities. Make sure students have a copy of the amino acids chart or distribute another chart.
After students have completed the activity review students answers to the questions. Then have them think, as a class or in small groups, about how this activity relates to earlier activities in which they were changing charge.
4. Revisit the Disease Sickle Cell Anemia. Finally, discuss with your students the possible connection between DNA and Sickle Cell Anemia.
Extensions
DNA transcription animation http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/ (May work best with Internet Explorer)[Advanced] The advantage of a redundant genetic code. Why would a biological system like DNA require 64 possible words-codons in the DNA if we need to code only 20 amino acids? This is not something students can infer. The answer, however, lies with the redundancy of the genetic code, which protects it from being misunderstood. Sometimes one of the nucleotides in the codon can be replaced or "misspelled", but the cell will be able still to interpret the codon correctly using the remaining two correct letters. (When you sometimes call Mother "Mam" or "Mum" or even "Mom", she may still reply recognizing the two Ms.) It is the same with proteins. In each set of three nucleotides (or codons), two are the same for a given amino acid, and one can vary, or "wobble." What's the point for a cell of that wobbling? Having several different codons to code the same amino acid gives a cell added protection against mutations. As a result, some substitutions of the nucleotides in a gene may not change the sequence of amino acids in a protein if the replaced nucleotide was the one that can wobble.
Index