Name: DNA Model Stations - Weebly

Name:DNA Model StationsDNA ReplicationIn this lesson, you will learn how a copy of DNA is replicated for each cell. You will model a 2Drepresentation of DNA replication using the foam nucleotide pieces.For the following activity, you will use the following DNA sequence.1. Use the base pairing rules (A-T/C-G) to write the complementary strand in the space below.CCGCATGTGTGAGATACATTGGCCAAGACACTGTTAGCTC2. Create this double strand of DNA using the grey foam pieces.DNA replication begins at a specific site called origins of replication. A eukaryotic chromosome mayhave hundreds or even a few thousand replication origins. Proteins that start DNA replication attach tothe DNA and separate the two strands, creating a replication bubble. At each end of the replicationbubble, is a Y-shaped region where the parental strands of DNA are being unwound. This region isreferred to as the replication fork.3. What is the name of the enzyme that separates the two strands of DNA? How do you know thatit is an enzyme?4. Why do you think multiple replication bubbles form during the process of DNA replication?Begin the process of DNA replication by feeding the strands ofthe constructed DNA into the helicase enzyme on thereplication mat. Be sure to position the 5’ and 3’ ends of theDNA appropriately as you place the DNA on the mat.Continue feeding the DNA through the enzyme until you have11 bases emerging from the helicase. Notice that helicasemoves into the replication fork, not away from it.5. What is the purpose of the helicase?

6. What type of bond is broken by the helicase?7. Why is he helicase able to break these bonds?Note: Replication occurs on both sides of the replication fork simultaneously. For simplicity andclarification, you will simulate replication on one side of the fork only.Continuous ReplicationThe DNA polymerase enzyme catalyzes thesynthesis of new DNA by adding nucleotides to apreexisting chain. New DNA can elongate only in the5’ 3’ direction. The DNA strand that is madecontinuously is referred to as the leading strand.Simulate replication in the leading strand by placingon DNA polymerase at the left of the replicationfork and adding colored nucleotides in the activesite to the parent strand. Continue addingnucleotides as you move the DNA polymerase untilyou reach the fork.8. Sketch a helicase on the diagram to the right andindicate the directionality of the newly replicatedleading strand of DNA.9. Will you be able to synthesize the other strand of DNAin a continuous manner when using the model?Explain why or why not. (Hint: think about thedirectionality of the DNA strands)To accommodate the 5’ 3’ synthesis of DNA, short fragments are made on the second strand, which isreferred to as the lagging strand. These fragments are called Okazaki fragments and are usually 100-200nucleotides long in Eukaryotic cells.10. Label the leading and lagging strands on thediagram.11. Why is DNA replication considered to be a semiconservative process?

12. How do these two new strands compare to the original (parental) strand?Protein Synthesis-TranscriptionAlmost all dynamic functions in a living organism depend on proteins. Proteins are molecular machinesthat perform a wide variety of essential functions. Scientists currently believe that there areapproximately 100,000 different proteins in the human body. Given the important role that thesemolecules play in an organism’s survival, it is understandable that scientists focus a considerableamount of attention studying them. Central to their study is the question of how these molecules areproduced in a cell. The molecular chain of command dictates the directional flow of genetic informationfrom DNA to RNA to protein was dubbed the central dogma by Francis Crick in 1956.DNA is the Universal CodeDNA carries all of the instructions for making the proteins found in our bodies. In fact, DNA is theuniversal code for the characteristics of simple organisms such as bacteria, and for complex organismssuch as plants and animals. DNA codes for the characteristics of all living things! DNA has only fournitrogen bases: A, T, G, and C. But there are 20 amino acids that serve as the building blocks(monomers) for all proteins. The key to deciphering DNA is called a triplet code, in which the sequenceof three adjacent DNA nitrogen bases (nucleotides) codes for a specific amino acid.1. Given that there are more possible combinations for amino acids than amino acids themselves,what does this imply about the number of codes for each amino acid?The process of deciphering DNA to produce a protein requires two major stages: (1) transcription and(2) translation. Transcription is the process in which DNA is used as a template to produce a singlestranded RNA molecule. Translation is the process in which the DNA code, now contained in the singlestranded RNA, is deciphered into a sequence of linked amino acids that become a protein.In eukaryotic cells, DNA is found in the nucleus, chloroplast, and mitochondria, and cannot leave thesestructures. As a result, transcription occurs inside these organelles in eukaryotic cells. Proteins aremade by ribosomes that are outside of the nucleus in the cytoplasm. The RNA must leave the nucleusand carry the code to the ribosome for proteins to be synthesized. The RNA carrying the code is calledmessenger RNA (mRNA).2. Use the base pairing rules (A-T/C-G) to write the complementary DNA strand in the space below.CCGCATATGTGTGAGATACATTGGCCAAGACACTGTTAGCTC3. Create this strand of DNA using the rounded DNA foam pieces.Transcription: InitiationLike DNA polymerases that function in DNA replication, RNA polymerases can assemble mRNA only in its5’ 3’ direction. In order for this to properly occur, the template strand of DNA must be oriented in thetop slot with the 3’ end (arrow end) entering the polymerase first.

4. Label the DNA template strand and the non-template strand in the photo.Transcription: ElongationFeed the DNA into the RNA polymerase. The strand that corresponds to the strand you wrote in above isthe template strand.5. What happens to the DNA strand when it enters the RNA polymerase? Why is this important?RNA polymerase uses the template strand of DNA to synthesize the mRNA. You will use the templatestrand of DNA to complementary base pair the correct sequence of mRNA nucleotides.6. What is the start codon found on the mRNA strand for protein synthesis?7. What is the corresponding nucleotide sequence on the DNA strand?8. When you reach the corresponding nucleotide sequence on the DNA strand, start adding RNAnucleotides according to the base pairing rules (A-U/C-G) to create a new strand of mRNA.Transcription: TerminationAt this point the mRNA will separate from the DNA and may be processed into its final form. Thetemplate strand of DNA will rejoin with the non-template strand. Complete this step with your model.9. Using your mRNA model, record the correct sequence of mRNA base pairs:Big IdeaThe sequence of nucleotides in your DNA encodes the sequence of amino acids in your proteins. Theoverall process of making a protein, using the information contained in a gene, is referred to as geneexpression. In the first step of this process-known as transcription-an RNA polymerase uses one strandof a gene as a template for the synthesis of a strand of messenger RNA. In the next step in this processknown as translation-the ribosome translates the sequence of nucleotides in the messenger RNA intothe sequence of amino acids that make up the protein.

Protein Synthesis: TranslationTranslationTranslation occurs in the cytoplasm of the cell and is defined as the synthesis of a protein (polypeptide)using information encoded in an mRNA molecule. In the process of protein synthesis there are twoimportant types of nucleic acids: DNA and RNA. Messenger RNA (mRNA) has the information forarranging the amino acids in the correct order to make a functional protein.The key to deciphering DNA is called a triplet code, in which the sequence of three adjacent DNAnitrogen bases (nucleotides) codes for a specific amino acid. Translation of the mRNA occurs in groupsof three nitrogenous bases called codons. The order in which the amino acids are put together dependson the sequence of bases in the mRNA. Proteins can consist of as few as 100 or as many as thousands ofamino acids.1. Using the codon chart, identify the amino acids that the following codons code for.Codon AUGUGUGAGAUACAUUGGCCAAGACACUGUUAGAminoAcidThe process of deciphering DNA to produce a protein requires two major stages: (1) transcription and(2) translation. Transcription is the process in which DNA is used as a template to produce a singlestranded RNA molecule. Translation is the process in which the DNA code, now contained in the singlestranded RNA, is deciphered into a sequence of linked amino acids that become a protein.In eukaryotic cells, DNA is found in the nucleus, chloroplast, and mitochondria, and cannot leave thesestructures. As a result, transcription occurs inside these organelles in eukaryotic cells. Proteins aremade by ribosomes that are outside of the nucleus in the cytoplasm. The RNA must leave the nucleusand carry the code to the ribosome for proteins to be synthesized. The RNA carrying the code is calledmessenger RNA (mRNA).The initiation stage of translation brings together mRNA and a second type of RNA called transfer RNA(tRNA), with two subunits of a ribosome. Two functional portions of the tRNA are necessary for proteinsynthesis to continue. One functional part of tRNA is a series of three nitrogen bases referred to as ananticodon. This anticodon forms complementary base pairs with the codon of the tRNA. The otherfunctional part of tRNA attaches to a specific amino acid.2. Identify the tRNA anticodon for the following codons.CodonAUGUGUGAGAUACAUUGGCCAAGACACUGU UAGAnticodon3. Add the appropriate foam amino acids to each of the foam tRNAs identified in the table above.4. Assemble the following strand of mRNA using the foam RNA GCUCTranscription: InitiationTo initiate protein synthesis, the AUG start codon of the mRNA is bound to the P site of the smallribosomal subunit. The initiation tRNA-charged with Met-base pairs with the AUG codon, and the large