Exploration RNA and Protein Synthesis

Name: Date: 2/9/21 Exploration: RNA and Protein Synthesis Directions: Follow the instructions to go through the simulation. Respond to the questions and prompts in the orange boxes. Vocabulary: amino acid, anticodon, codon, gene, messenger RNA, nucleotide, ribosome, RNA, RNA polymerase, transcription, transfer RNA, translation Prior Knowledge Questions (Do these BEFORE using the Gizmo.) 1. Suppose you want to design and build a house. How would you communicate your design plans with the construction crew that would work on the house? I believe that the best way to communicate the plans or a blueprint with the construction crew is to develop plans for the house under construction and make multiple copies for the crew. 2. Cells build large, complicated molecules, such as proteins. What do you think cells use as their “design plans” for proteins? Cell uses DNA as plans for building proteins. In addition to DNA, another nucleic acid, called RNA, is involved in making proteins. DNA and RNA to construct a protein out of amino acids Gizmo Warm-up Just as a construction crew uses blueprints to build a house, a cell uses DNA as plans for building proteins. In addition to DNA, another nucleic acid, called RNA, is involved in making proteins. In the RNA and Protein Synthesis Gizmo, you will use both DNA and RNA to construct a protein out of amino acids. 1. DNA is composed of the bases adenine (A), cytosine (C), guanine (G), and thymine (T). RNA is composed of adenine, cytosine, guanine, and uracil (U). Look at the SIMULATION pane. Is the displayed segment a part of a DNA or RNA molecule? How do you know? DNA because it has the base A-T and G-C, whereas RNA has the base A-U and G-C. DNA has thymine instead of uracil. 2. RNA polymerase is a type of enzyme. Enzymes help chemical reactions occur quickly. Click the Release enzyme button, and describe what happens. t split the DNA into two strands and breaks the hydrogen bonds between the nitrogenous bases Activity A: Transcription Get the Gizmo ready: ● If necessary, click Release enzyme. Introduction: The first stage of building a protein involves a process known as transcription. In transcription, a segment of DNA serves as a template to produce a complementary strand of RNA. This complementary strand is called messenger RNA, or mRNA. Question: What occurs during transcription? 1. Experiment: Like DNA, RNA follows base-pairing rules. Experiment to find which RNA nucleotide on the right side of the Gizmo will successfully pair with the thymine at the top of the template strand of DNA. (NOTE: The DNA on the right side is the template strand.) Which RNA base bonded with the thymine? Adenine 2. Experiment: The next three bases on the DNA template strand are adenine, cytosine, and guanine. Use the Gizmo to answer the following questions: A. Which RNA base bonds with adenine? Uracil B. Which RNA base bonds with cytosine? Guanine C. Which RNA base bonds with guanine? Cytosine 3. Observe: In molecules of RNA, uracil takes the place of the DNA base Thymine 4. Build: Continue building the strand of mRNA until you have used all of the RNA nucleotides. What is the nucleotide sequence of the mRNA strand you built? AUG CUG ACC UAG 5. Apply: Suppose a template strand of DNA had the following sequence: T A C G G A T A A C T A C C G G G T A T T C A A What would be the complementary strand of mRNA? A U G C C U A U U G A U G G C C C A U A A G U U 6. Predict: How would a change to the sequence of nucleotides in a DNA segment affect the mRNA transcribed from the DNA? The template strand and the complementary strange would change. The information on the mRNA will change creating a different protein, or a mutation. Any change in DNA is reflected in the mRNA. Activity B: Translation Get the Gizmo ready: ● Once the mRNA strand has been built, click Continue. Introduction: After a strand of mRNA has been built, the strand exits the cell’s nucleus. The second stage of protein synthesis, called translation, occurs next. During translation, the strand of mRNA is used to build a chain of amino acids. Question: What occurs during translation? 1. Observe: Examine the strand of mRNA on the SIMULATION pane. Every group of three bases of mRNA is called a codon. In the table at right, list the nitrogen bases in each codon. (Hint: Start from the top of the strand and read down.) The first mRNA codon is called the universal start codon. Codon mRNA bases 1 AUG 2 CUG 3 ACC 4 UAG 2. Predict: Translation starts when a ribosome (the purple structure on the SIMULATION pane) binds to a strand of mRNA. Transfer RNA, or tRNA, begins bringing amino acids into the ribosome. Each tRNA molecule carries only one kind of amino acid. This amino acid is determined by the tRNA’s anticodon, a set of three unpaired bases. Use the Gizmo to check your answer. Which anticodon do you think would attach to the mRNA’s start codon? UAC 3. Observe: Place the next two tRNA molecules on the mRNA strand. What happens? The amino acid chain is released from the tRNA. When the next anticodons is placed the previous one is released. As each tRNA molecule binds to the mRNA, the ribosome joins the amino acid carried by the tRNA to the growing amino acid chain. 4. Describe: UAG (as well as UAA and UGA) is an example of a stop codon. Molecules called release factors bind to stop codons. Place the release factor on the mRNA molecule. What happens? The molecules go away, and a protein is created. All the anticodons are released, leaving protein left with the mRNA Click Continue. Your protein is now complete. Most actual proteins consist of sequences of hundreds of amino acids. 5. Infer: Why do you think stop and start codon signals are necessary for protein synthesis? Start codons are what starts the process of making proteins. The stop codon is what finishes off the protein. Without knowing where to end/begin, the mRNA might copy a sequence unnecessary to the protein, possibly affecting its function, and the process of creating it. The genetic codes are specific and important to ensure the function of each protein. 6. Summarize: Describe the processes of transcription and translation in your own words, based on what you have observed in the Gizmo. Transcription: A complimentary mRNA strand is made using one of the original DNA strands. This is the synthesis of an RNA strand from a DNA template. A gene's protein building instructions are transcribed to mRNA. mRNA carries the code from DNA to the ribosomes where translation into a protein occurs. It is copying the code in the DNA to a messenger strand of RNA, substituting Uracil for Thymine. RNA polymerase split the DNA. The RNA is identical to the DNA, except it has uracil instead of thymine. Once completed, the mRNA splits from the DNA. Translation: Extension: Genes and traits In translation mRNA is decoded by a ribosome, outside the nucleus, to produce a specific amino acid chain. tRNA molecules bring on anticodon and an amino acid to the ribosome. The amino acids are strung together to create proteins. The RNA molecule moves away from the. Then transcriptional RNA anti-codons help create proteins. In the end, the protein is released. The new protein is enclosed in a vesicle and transported to where it is needed. Get the Gizmo ready: ● You will not need to use the Gizmo for this activity. Introduction: Inside a ribosome, amino acids are linked together to form a protein molecule. As the chain of amino acids grows, it folds and coils to form a three-dimensional shape. The complex shape that results determines the properties of the protein. Proteins have a wide variety of structures and perform many essential functions in living things. A sequence of DNA that codes for a specific protein is called a gene. By coding for proteins, genes determine an organism’s inherited traits. Question: How do genes code for specific proteins and traits? 1. Translate: Each codon codes for one of 20 amino acids. This code is universal among all living things. For example, the mRNA codon GGU codes for the amino acid glycine in every living thing, from a bacteria to an elephant. Examine the codon chart below. The amino acid coded for by a specific mRNA codon can be determined by finding the first base of the codon along the left side of the table, the second base along the top of the table, and the third base along the right side of the table. What amino acids do the following codons code for? AUG: Methionine CUG: Leucine ACC: Threonine UAG: Stop 2. Apply: Suppose you wanted a protein that consists of the amino acid sequence methionine, asparagine, valine, and histidine. Give an mRNA sequence that would code for this protein. A U G A A U G U C C A C 3. Summarize: How do genes determine the traits of an organism? Explain in detail. Trait on an organism displays are determined by the genes that is inherited form the parents. It offsets errors, because if there is a mistake in letters it will still code for the same protein. If an error in translation/transcription happens for every 100 000 – 1 000 000 nucleotides, then the number of actual errors and flawed proteins will be decreased, if multiple codons code for the same proteins. The traits an organism displays are ultimately determined by the genes it inherited from its parents, in other words, its genotype 4. Extend your thinking: Sometimes errors occur during transcription or translation. Examine the codon chart on the previous page. Notice that each amino acid is coded for by several different codons. For example, alanine is coded for by GCU, GCC, GCA, and GCG. How might this offset transcription or translation errors? It offsets them being errors because there are many codons so even if there is a mismatch pairing of the letters there could be another codon with those letters resulting in it not becoming an issue or causing a bad mutation. This basically decreases the chance that a transcription/translation could cause a flawed protein to form. 5. Think and discuss: Consider the two following statements: ● The theory of evolution states that all living things had a single common ancestor. ● The translation between mRNA and amino acids is the same for all living things. (For example, the mRNA codon CAG codes for glutamine in all living things.) Does the second statement support the theory of evolution? Explain why or why not. If possible, discuss your answer with your teacher and classmates. No, since there are different codons for one amino acid, they could all be different from each other. Yes, the second statement does support the theory of evolution. All the organisms on Earth share a common universal genetic code. The genetic code is made of the same nucleotides which are adenine, guanine, cytosine and thymine. The m RNA produced from the genetic code makes the same proteins in each organism. This similarity between the genetic code of every organism on the Earth shows that all organisms might have evolved from a common ancestor. Through evolution, the changes in the sequence of the genetic code caused differences among the organisms. If different groups of living things were not related to one another, it would be likely that transcription would work differently as well. The fact that transcription is the same for all living things is strong evidence that all living things are related and may have descended from a single ancestor