structure and function of DNA.DNA and Protein Synthesis
\nReview the safety materials and wear goggles when
\nworking with chemicals. Read the entire exercise
\nbefore you begin. Take time to organize the materials
\nyou will need and set aside a safe work space in
\nwhich to complete the exercise.
\nExperiment Summary:
\nYou will learn the structure and function of DNA and
\nRNA. You will learn the similarities and differences
\nbetween DNA and RNA. You will learn the process
\nof protein synthesis and create and use models to
\ndemonstrate both transcription and translation.
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\nEXPERIMENT
\nLearning Objectives
\nUpon completion of this laboratory, you will be able to:
\n\u25cf Review the structure and function of DNA.
\n\u25cf Identify the codons that code for amino acids in DNA and RNA.
\n\u25cf Explain the purpose of start and stop codons in protein synthesis.
\n\u25cf Summarize the steps involved in protein synthesis and define a ribosome and its three sites.
\n\u25cf Summarize the steps of transcription, including: initiation, elongation, and termination.
\n\u25cf Summarize the steps of translation, including; initiation, elongation, and termination.
\n\u25cf Illustrate and model the processes of transcription and translation.
\n\u25cf Construct a series of tRNA molecules and write the anti-codons and amino acids each tRNA
\ncarries.
\n\u25cf Explain the difference in the number of amino acids that were present at the start and at the
\nend of the translation model.
\nTime Allocation: 3 hours
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\nExperiment DNA and Protein Synthesis
\nMaterials
\nStudent Supplied Materials
\nQuantity Item Description
\n1 Camera, digital or Smartphone
\n1 Pair of scissors
\n1 Printer
\n10 Sheets of printer paper
\n1 Pen or pencil
\n1 Tape
\nHOL Supplied Materials
\nQuantity Item Description
\n1 DNA Nucleotide Template
\n1 RNA Nucleotide Template
\n1 tRNA Template
\nNote: To fully and accurately complete all lab exercises, you will need access to:
\n1. A computer to upload digital camera images.
\n2. Basic photo editing software such as Microsoft Word\u00ae or PowerPoint\u00ae, to add labels, leader
\nlines, or text to digital photos.
\n3. Subject-specific textbook or appropriate reference resources from lecture content or other
\nsuggested resources.
\nNote: The packaging and\/or materials in this LabPaq kit may differ slightly from that which is listed
\nabove. For an exact listing of materials, refer to the Contents List included in your LabPaq kit.
\nwww.HOLscience.com 3 \u00a9Hands-On Labs, Inc.
\nExperiment DNA and Protein Synthesis
\nBackground
\nDNA, Codons, and Proteins
\nDeoxyribonucleic acid (DNA), the genetic material of all living organisms, is composed of two
\nchains of nucleotides wound together in a double-helical formation. Nucleotides, the molecules
\nresponsible for the structural units of DNA, are composed of three sections: a phosphate
\ngroup (PO4
\n), a sugar (deoxyribose) group, and a nitrogenous base. There are four different DNA
\nnucleotides: adenine (A), thymine (T), cytosine (C), and guanine (G), which are identical in their
\nphosphate and sugar groups, but vary in their nitrogenous bases. The bonds between the sugar
\nand phosphate groups of each nucleotide form the sugar-phosphate backbone of DNA and the
\ntwo strands wind together as a result of base pairing: AT (Adenine-Thymine) or GC (GuanineCytosine).
\nThe arrangement of the four DNA nucleotides creates the genetic code, the blueprint for all living
\nthings. The genetic code is composed of codons, triplets of nucleotides that contain the code for
\nthe production of amino acids, which are strung together to create proteins (polypeptide chains).
\nProteins are highly complex, organic substances that provide a vast number of functions in living
\norganisms, including maintenance of cells and growth. Thus, proteins are essential components
\nof living tissues including: skin, bones, and muscle. The four different nucleotides provide 64
\ndifferent codons (four options for each of three positions = 43
\n= 64 options), which code for one
\nof twenty amino acids or a stop codon. See Table 1.
\nTable 1. Codon Chart (DNA)
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\nExperiment DNA and Protein Synthesis
\nProtein Biosynthesis and Transcription
\nProtein biosynthesis is the process where cells use the genetic code to build proteins. The process
\ndiffers slightly between prokaryotes (single-celled organism with no organelles or distinct nucleus)
\nand eukaryotes (single or multi-celled organisms with organelles and DNA contained in a distinct
\nnucleus). In the context of this experiment, the focus will be on the main steps and commonalities
\nbetween the prokaryotic and eukaryotic protein biosynthesis steps. There are two main steps in
\nprotein biosynthesis: transcription and translation.
\nTranscription is the process by which single stranded RNA is synthesized from DNA. RNA
\n(ribonucleic acid), like DNA, is composed of nucleotides with a phosphate, a sugar (ribose), and
\none of four nitrogenous bases. The nucleotides adenine, cytosine, and guanine exist in both DNA
\nand RNA, however; in RNA, the nucleotide uracil (U) replaces thymine (T), and binds with adenine
\n(A). See Figure 1.
\nFigure 1. Nitrogenous bases in DNA and RNA. Note that while DNA is double-stranded, RNA
\nexists as a single-strand. \u00a9 udaix
\nThere are three steps in transcription: initiation, elongation, and termination. A general depiction
\nof transcription is shown in Figure 2.
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\nExperiment DNA and Protein Synthesis
\nFigure 2. General schematic of transcription. \u00a9 The National Human Genome Research Institute
\nIn initiation, an enzyme called RNA polymerase binds to the DNA promoter, which is the DNA
\nsequence that initiates transcription. The RNA polymerase causes the two strands of DNA to begin
\nunwinding and separate from one another. In elongation, the RNA polymerase travels downstream
\n(3\u2019 to 5\u2019) along the DNA antisense strand, elongating the mRNA transcript in the 5\u2019 to 3\u2019 direction.
\nThe DNA antisense strand is the template strand from which the mRNA is transcribed. Figure
\n2 illustrates how transcription creates an mRNA copy of the DNA sense, or coding, strand, with
\nuracil replacing thymine in the newly constructed mRNA. As the RNA polymerase continues to
\nmove downstream, the two strand of DNA re-wind into a double-helix formation. In termination,
\nthe RNA polymerase detaches from the DNA and releases the transcribed mRNA. In a prokaryote,
\nthe released mRNA is complete and ready to move into translation, while in a eukaryote the
\nreleased RNA undergoes a series of steps where it is processed before moving into translation as
\nmRNA.
\nTranslation
\nTranslation, the second main step of protein synthesis, is the process by which the mRNA (created
\nin transcription) is converted into a protein. In a prokaryote, translation occurs in the cytoplasm,
\nthe same site as transcription; while in eukaryotes, translation occurs in the cytoplasm, where
\nit is carried after transcription has completed in the nucleus. There are two major players in
\ntranslation; transfer RNA (tRNA) and ribosomes. tRNA is a clover-shaped molecule that acts as the
\ninterpreter between mRNA and the protein it will help to synthesize. A ribosome is an organelle
\nwhich functions as the site of protein synthesis. Ribosomes are made of ribosomal RNA (rRNA)
\nand protein molecules, and are divided into two subunits: large and small. The small ribosomal
\nwww.HOLscience.com 6 \u00a9Hands-On Labs, Inc.
\nExperiment DNA and Protein Synthesis
\nsubunit binds the mRNA and reads the information contained in the mRNA nucleotide sequence.
\nThe large ribosomal subunit contains three binding sites: the peptidyl-tRNA site (P site), the
\naminoacyl-tRNA site (A site), and the exit site (E site). See Figure 3.
\nFigure 3. The ribosome.
\nThere are three steps in translation: activation and initiation, elongation, and termination. A
\ngeneral depiction of translation is shown in Figure 4.
\nFigure 4. General schematic of translation.
\nIn the first step of translation, activation and initiation, the mRNA is threaded between the
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\nExperiment DNA and Protein Synthesis
\nsmall and large subunits of the ribosome. The ribosome signals the start of translation when it
\nencounters and binds to the first start codon (AUG, which codes for the amino acid methionine)
\nat the A site. The tRNA carrying the anticodon (UTC) and the methionine binds to the mRNA
\ncodon at the ribosomal A site, creating the initiation complex, signaling translation to begin.
\nThe tRNA bound mRNA then moves into the P site, which brings in the next tRNA carrying the
\ncomplementary anticodon and amino acid to the mRNA now in the A site.
\nThe amino acid in the P site then forms a peptide bond with the amino acid in the A site,
\nreleasing the amino acid from the tRNA in the P site and moving the empty tRNA into the E site.
\nSimultaneously, the tRNA in the A site, holding the two peptide-bonded amino acids, then moves
\ninto the P site, signaling the next tRNA to bind to the mRNA in the A site. Using Figure 4 as an
\nexample, as the empty tRNA (which had been carrying valine) exits the E site, a peptide bond is
\nformed between lysine (in the P site) and cysteine (in the A site). The lysine (peptide bound to
\nvaline, glutamate, serine, and glycine) then detaches from the tRNA in the P site and attaches to
\nthe tRNA in the A site. The tRNA in the A site (now carrying the cysteine, lysine, valine, glutamate,
\nserine, and glycine) then moves into the P site, releasing the tRNA that had carried the lysine from
\nthe E site. As the tRNA is released from the E site, tRNA carrying the anticodon AUA and the amino
\nacid tyrosine (yellow Tyr) binds to the mRNA in the A site, continuing the process. This continuous
\nprocess, called elongation, builds the polypeptide chain (protein) one amino acid at a time until
\nthe mRNA reads a stop codon (UAA, UAG, or UGA).
\nWhen a stop codon is encountered in the mRNA at the A site, termination is signaled. In
\ntermination the stop codon signals the end of elongation, which cleaves the protein from the
\ntRNA, allowing it to exit the ribosome. The two ribosome subunits and the mRNA then dissociate
\nfrom one another, completing the translation process. The protein then undergoes a series of
\nsteps including post-translational modifications and protein folding to assume its new shape.
\nIn 2009, Dr. Ada Yonath won the
\nNobel Prize in Chemistry. She was the first
\nwoman to win the Nobel Prize in Chemistry
\nin 45 years, since Dorothy Crowfoot Hodgkin
\nin 1964, and the first woman in the Middle East
\nto ever win the Chemistry Nobel Prize. Her award,
\nshared with Dr. Thomas Steitz and Dr. Venkatraman
\nRamakrishnam, was the result of her work on the
\nstructural determination of the ribosome, determining
\nthe structure of both the small and large ribosomal
\nsubunits. Her work lead to the conclusion that a
\nribosome is a ribozyme (ribonucleic acid enzyme), that
\norganizes its substrates in the stereochemistry necessary
\nfor the formation of peptide bonds. From her work
\ncame the new and exciting crystallization technique
\ncalled cryo bio-crystallography, which allows for the
\ncrystallization of large biological macromolecules at
\ncryogenic temperatures (approximately -320\u00b0F)
\nallowing the macromolecules to maintain
\ntheir solution state.
\nwww.HOLscience.com 8 \u00a9Hands-On Labs, Inc.
\nExperiment DNA and Protein Synthesis
\nExercise 1: Protein Synthesis
\nIn this exercise, you will model the steps of protein synthesis, starting with a single strand of
\nnucleotides and ending with a protein.
\n1. Print 6 copies of the DNA Nucleotide Template, 4 copies of the RNA Nucleotide Template, and
\n1 copy of the tRNA Template. It is preferable, but not necessary, to print them in color. The
\ntemplates are located in the \u201cSupplemental Documents\u201d folder of your digital courseware.
\n2. Review the coding strand of DNA (5\u2019 to 3\u2019) in Data Table 1 of your Lab Report Assistant.
\n3. Create the template strand of DNA (3\u2019 to 5\u2019) and record in Data Table 1.
\n4. Gather the scissors, tape, and the 6 printed copies of the DNA Nucleotide Template. Cut out
\nthe nucleotides from the template. It is not necessary to cut out the entire nucleotide; rather,
\ncut the nucleotide in a rectangular shape, only cutting out the details of the nitrogenous
\nbases. See Figure 5.
\nFigure 5. Cutting out DNA nitrogenous bases.
\n5. Using the DNA nucleotides, create the entire double strand of DNA by matching up and taping
\ntogether the base pairs. See Figure 6 as an example.
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\nExperiment DNA and Protein Synthesis
\nFigure 6. Pairing of DNA nucleotides.
\n6. Take a photograph of the completed double strand of DNA with your name and the data
\nshowing in the photograph. Resize and insert the photograph into Data Table 2 of your Lab
\nReport Assistant. Refer to the appendix entitled \u201cResizing an Image\u201d for guidance with resizing
\nan image.
\n7. Determine the mRNA strand that transcription would produce from the DNA template strand
\nand record the mRNA strand in Data Table 1.
\n8. Gather the 4 printed copies of the RNA Nucleotide Template. Cut out the nucleotides from
\nthe template. It is not necessary to cut out the entire nucleotide; rather, cut the nucleotide in
\na rectangular shape, only cutting out the details of the nitrogenous bases.
\n9. Using the RNA nucleotides, create the mRNA strand by matching up and taping together the
\nbase pairs.
\n10. Take a photograph of the mRNA strand with your name and the date showing in the photograph.
\nResize and insert the photograph in Data Table 2.
\n11. Starting with the first mRNA nucleotide, determine what amino acids the codons in the mRNA
\nare coding for and record in Data Table 1.
\nNote: Use Table 2 to determine the amino acids coded by RNA codons.
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\nExperiment DNA and Protein Synthesis
\nTable 2. Codon Chart (RNA)
\n12. Gather the printed copy of the tRNA Template and cut out the tRNAs.
\n13. Build the line of tRNAs that would flow into the A site during translation. Write the anticodons
\ninto each tRNA and the amino acid the mRNA codes for. See Figure 7 as an example of
\nthe tRNA that would be created from the mRNA codons CCU.
\nNote: Use Figure 4 in the Background section as needed to help organize your thoughts and identify
\nwhere in the mRNA strand translation would begin.
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\nExperiment DNA and Protein Synthesis
\nFigure 7. tRNA created from mRNA (CCU). Note that the anti-codons (GGA) and the name of the
\namino acid (gly = glycine) are written into the tRNA.
\n14. Take a photograph of the tRNAs (in order) with your name and the date showing in the
\nphotograph. Resize and insert the photograph in Data Table 2.
\n15. Write the name of the each amino acid in the final protein created from translation and record
\nin Data Table 1.
\n16. When you are finished uploading photos and data into your Lab Report Assistant, save your
\nfile correctly and zip the file so you can send it to your instructor as a smaller file. Refer to the
\nappendix entitled \u201cSaving Correctly\u201d and the appendix entitled \u201cZipping Files\u201d for guidance
\nwith saving the Lab Report Assistant correctly and zipping the file.
\nNote: Use a textbook or internet source, as necessary, for a list of the three-letter amino acid
\nabbreviations and the full amino acid names.
\nQuestions
\nA. How many amino acids were coded for by the mRNA How many amino acids were present
\nin the final protein chain created in translation In detail, explain the differences in the two
\nnumbers; why were some amino acids coded for by the mRNA but not present in the final
\nprotein chain What amino acids were omitted from the final protein chain Explain your
\nanswers.<\/p>\n
Experiment DNA and Protein Synthesis<\/p>\n","protected":false},"excerpt":{"rendered":"
structure and function of DNA.DNA and Protein Synthesis Review the safety materials and wear goggles when working with chemicals. Read the entire exercise before you begin. Take time to organize the materials you will need and set aside a safe Read More …<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[],"tags":[],"class_list":["post-95612","post","type-post","status-publish","format-standard","hentry"],"_links":{"self":[{"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/posts\/95612","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/comments?post=95612"}],"version-history":[{"count":0,"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/posts\/95612\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/media?parent=95612"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/categories?post=95612"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.benedictsol.com\/blogs\/wp-json\/wp\/v2\/tags?post=95612"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}