AP Biology - Protein Synthesis Lab (Teacher Copy)

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NameAP BiologyPeriodDateLAB : PROTEIN SYNTHESIS — TRANSCRIPTION AND TRANSLATIONDNA is the molecule that stores the genetic information in your cells. That information is codedin the four bases of DNA: C (cytosine), G (guanine), A (adenine), and T (thymine). The DNAdirects the functions of the cell on a daily basis and will also be used to pass on the geneticinformation to the next generation. Because of its critical role in all the functions of the cell, DNAis kept protected in the nucleus of your cells.DNA is organized in sections called genes. Genes code for proteins, and it is proteins that doall the work in the cell. They function as structural proteins — serving as the building blocks ofcells and bodies. And they function as enzymes — directing all the chemical reactions in livingorganisms.Proteins are made in the cytoplasm by ribosomes. Since DNA cannot leave the nucleus, theinformation from DNA must be transmitted from the nucleus to the cytoplasm. Duringtranscription, each gene on the DNA is read and codes directly for a messenger RNA(mRNA) molecule. The mRNA is made by matching its complementary bases — C, G, A, and U(uracil) — to the DNA bases. This process is called transcription, because the message isgoing from one version of nucleic acid language (DNA code) to another version of nucleic acidlanguage (RNA code), so it is like transcribing from the key of G to the key of C in music. Beforeleaving the nucleus, this primary mRNA transcript is modified in several ways. Introns(intervening non-coding units) are edited out and exons (expressed coding sequences) arespliced together. In addition, a 5′ GTP cap and a 3′ poly-A tail are added to the mRNA toprotect it from RNase enzymes in the cytoplasm. This mature mRNA transcript then leaves thenucleus and carries the code for making the protein from the DNA gene in the nucleus to theribosome in the cytoplasm.During translation, the ribosome reads the sequence of bases on the mRNA in sets of three —the triplet codons. Another type of RNA — transfer RNA (tRNA) — brings the protein buildingblocks — amino acids — to the ribosome as they are needed. The ribosome bonds the aminoacids together to build the protein coded for by the gene back in the nucleus. This process iscalled translation, because the message is going from nucleic acid language (DNA/RNA code)to the completely different amino acid language (protein code), so it is like translating fromEnglish to Chinese.PROCEDURE1. Obtain the cardstock with 4 sections of DNA. Cut the strips out along straight lines and tapethem together to make a long one-sided DNA molecule. Each section is numbered. Laythem out on the desk from left (#1) to right (#4). See the diagram below. This will form onelong strand of DNA and will serve as the template strand of our gene.DNA2. We are going to use this section of our DNA as a gene to be transcribed and then translatedinto a protein the cell needs. Remember it used to be part of a double-stranded DNA1 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biologymolecule. But it has already been unzipped and now will be used as the template to buildmRNA, one base at a time. So first design an RNA polymerase enzyme to do this mRNAsynthesis job.3. You have also been supplied with mRNA nucleotides. Build a mRNA molecule, one base ata time, from this gene by transcribing your DNA template. Don’t forget to only starttranscribing downstream from the TATA box promoter sequence. As you are transcribing,tape this mRNA molecule along its length to simulate the covalent bonds between bases.This way, it will be a stable molecule and can be moved off of the DNA to the ribosome fortranslation in the cytoplasm. Do not tape the mRNA to the DNA! Remember it has to leavethe DNA in the nucleus and travel to the ribosome in the cytoplasm. Follow the diagrambelow.DNAmRNA4. You have just made a primary transcript. It must be processed so it successfully travels tothe ribosome in the cytoplasm. Although we will not be simulating intron and exon splicingin this lab, you do need to add a 5′ GTP cap and a 3′ poly-A tail to the mRNA to protect themRNA. Although poly-A tails may be 20-100 bases long, add 6 adenine bases for yoursimulated poly-A tail.5. To be ready for the mRNA in the cytoplasm, design a ribosome to usein your simulation. Be sure to distinguish the small and largeribosomal subunits and mark the A, P, and E sites of the ribosome.6. To help the ribosome do its job, use a pencil to draw lines whichdivide your mRNA into triplet codons. Now obtain tRNA molecules and write in thecomplementary anticodons to match your mRNA codons so that the tRNAs bring the correctamino acid to the ribosome.7. Label the name of the amino acid that each tRNA is carrying. To help you with this, use themRNA codon chart and the amino acid code chart supplied by your teacher. Start readingthe mRNA at the START codon and end at the STOP codon. Follow the diagram below.2 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biologygrowing proteinmRNA8. As the tRNA molecules match the mRNA codons, cut off the amino acid and bond themtogether in a chain to simulate the action of the ribosome — covalently bonding the aminoacids in a polypeptide chain. Show your completed mRNA and your polypeptide to yourteacher for credit.Teacher’s Initials9. Use your DNA, your mRNA, and your polypeptide to answer the Summary Questions.3 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP BiologySUMMARY QUESTIONS1. Record the gene sequence (downstream from the TATA box) of the DNA strand (from 3′ to 5′) that coded for your 2425262728293031323334353637383940414243444546472. Record the sequence of the mRNA strand (from 5′ to 3′) that you built from the DNA in this 23334353637383940414243444546473. Divide the mRNA sequence into the triplet codons and list them in order 32425262728294. Record the amino acid sequence that this mRNA coded for.12345678910118910115. Record the tRNA anti-codons that carried the amino acids to the ribosome.12345674 of 11Developed by Kim B. Foglia www.ExploreBiology.com 200847

NameAP BiologyMUTATIONSSometimes when DNA is copied (replicated) errors occur. We call these mutations. When these mutations occur in gametes, theyhave the potential of being passed on to offspring and therefore will affect the next generation. Sometimes mutations cause onlyminor changes to a gene and therefore make only minor changes in the protein produced from that gene. These types of mutationsmay cause only minor effects to the phenotype of an organism. But sometimes mutations can cause great changes to the gene andtherefore greatly alter the protein that is made from that gene. This will likely have great effects on the organism, since the protein willnot be able to perform its normal function. This may lead to the inheritance of a genetic disease.6. POINT MUTATION 1: One mutation is called a point mutation where only one base in the DNA is copied incorrectly during DNAreplication. Here is your original DNA sequence from this lab and the amino acid sequence that was translated from 2526272829303132333435363738394041424344454647C T G A G C T A C T G A G C T G A G C T G C A G A G C C G A G C T C C T G T G T A A A C T T GMETTHRARGLEUASPVALSERALAARGGLYHISILESTOPa. Let’s simulate a point mutation at the 24th base. It was accidentally changed during replication from a G to a C.Now transcribe this new DNA strand into mRNA, and then translate it into its amino acid 47C T G A G C T A C T G A G C T G A G C T G C A C A G C C G A G C T C C T G T G T A A A C T T Gb. Did this change in the DNA sequence cause any significant change to the protein produced? Explain.5 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biologyc. What is the name of this type of point mutation and why is it referred to by this terminology?7. POINT MUTATION 2: Here is your original DNA sequence from this lab and the amino acid sequence that was translated from 2526272829303132333435363738394041424344454647C T G A G C T A C T G A G C T G A G C T G C A G A G C C G A G C T C C T G T G T A A A C T T GMETTHRARGLEUASPVALSERALAARGGLYHISILEa. Now, let’s simulate a point mutation at the 13th base. It was accidentally changed during replication from atranscribe this new DNA strand into mRNA, and then translate it into its amino acid sequence.STOPG to an 222324252627282930313233343536373839414243454647C T G A G C T A C T G A A C T G A G C T G C A G A G C C G A G C T C C T G T G T A A A C T T Gb. Did this change in the DNA sequence cause any significant change to the protein produced? Explain.6 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biologyc. What is the name of this type of point mutation and why is it referred to by this terminology?8. POINT MUTATION 3: Here is your original DNA sequence from this lab and the amino acid sequence that was translated from 2526272829303132333435363738394041424344454647C T G A G C T A C T G A G C T G A G C T G C A G A G C C G A G C T C C T G T G A C T A G C T GMETTHRARGLEUASPVALSERALAARGGLYHISILEa. Finally, let’s simulate a point mutation at the 21st base. It was accidentally changed during replication from atranscribe this new DNA strand into mRNA, and then translate it into its amino acid sequence.STOPG to an T. 2526272829303132333435363738394041424344454647C T G A G C T A C T G A G C T G A G C T T C A G A G C C G A G C T C C T G T G T A A A C T T Gb. Did this change in the DNA sequence cause any significant change to the protein produced? Explain.7 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biologyc. What is the name of this type of point mutation and why is it referred to by this terminology?d. Why could a mutation in a gamete have more profound biological consequences than a mutation in a somatic cell?9. Sickle cell anemia is an example of a genetic disease caused by a point mutation.a. Describe the specific DNA changes that produce the abnormal sickle cell hemoglobin.b. Explain the structural effect that this point mutation has on the hemoglobin protein.c. Explain why the sickle cell mutation is selected for in certain areas of the world.8 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biology10. FRAMESHIFT MUTATION 1: Another group of mutations is called frameshift mutations where at least one base is eitheradded to or deleted from the DNA as it is copied during DNA replication. Let’s investigate the effects of these.a. Here is your original DNA sequence from this lab and the amino acid sequence that was translated from 29303132333435363738394041424344454647C T G A G C T A C T G A G C T G A G C T G C A G A G C C G A G C T C C T G T G T A A A C T T GMETTHRARGLEUASPVALSERALAARGGLYHISILESTOPb. Let’s simulate a frameshift mutation by adding an additional base between the 36th & 37th bases. The base A wasaccidentally added to the sequence of the gene. Now transcribe this new DNA strand into mRNA, and then also translate itinto its amino acid 26272829303132333435363738394041424344454647C T G A G C T A C T G A G C T G A G C T G C A G A G C C G A G C T C C T A G T G T A A A C T T Gc. Did this change in the DNA sequence cause any significant change to the protein produced? Explain.d. Why are insertions and deletions called “frameshift” mutations, and what is meant by the “reading frame” of a gene?9 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biology11. FRAMESHIFT MUTATION 2: Here is your original DNA sequence from this lab and the amino acid sequence that was translatedfrom 29303132333435363738394041424344454647C T G A G C T A C T G A G C T G A G C T G C A G A G C C G A G C T C C T G T G T A A A C T T GMETTHRARGLEUASPVALSERALAARGGLYHISILESTOPa. Now let’s simulate a frameshift mutation by deleting the 10th base. Now transcribe this new DNA strand into mRNA, and thenalso translate it into its amino acid sequence.123456789C T G A G C T A 435363738394041424344454647G A G C T G A G C T G C A G A G C C G A G C T C C T G T G T A A A C T T Gb. Did this change in the DNA sequence cause any significant change to the protein produced? Explain.c. Which do you think would cause a more profound biological impact: (1) a deletion/insertion near the beginning of a gene, or(2) a deletion/insertion towards the end of a gene? Explain.10 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

NameAP Biology12. Cystic fibrosis is an example of a genetic disease caused by a frameshift mutation.a. Describe the specific DNA changes that produce the abnormal cystic fibrosis protein (the delta F508 mutation).b. Explain the structural and functional effects that this frameshift mutation has on lung cells.c. Explain why cystic fibrosis shortens life span.13. Are mutations always deleterious? What is the evolutionary value of mutations? Explain.11 of 11Developed by Kim B. Foglia www.ExploreBiology.com 2008

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LAB _: PROTEIN SYNTHESIS — TRANSCRIPTION AND TRANSLATION DNA is the molecule that stores the genetic information in your cells. That information is coded in the four bases of DNA: C (cytosine), G (guanine), A (adenine), and T (thymine). The DNA directs the functions of the cell on a

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Protein synthesis in cell-free extracts helped to crack the genetic code and has been extensively used to dissect ribosomal protein biosynthesis, providing a specialized niche for the development of these meth-ods. However, advances in cell-free protein synthesis in recent years, particularly the ability to reconstitute protein synthesis from .

with the answers in red font. Topics Covered: Protein synthesis, transcription, translation, amino acids, ribosomes, tRNA, mRNA, nucleotides etc. Check out the worksheet that goes along . Simulating Protein Synthesis fmfranco com. Protein Synthesis Simulation Lab Worksheet for 9th 12th. Investigation 14 Protein Synthesis Worksheet Answer Key.

Biology Lab Notebook Table of Contents: 1. General Lab Template 2. Lab Report Grading Rubric 3. Sample Lab Report 4. Graphing Lab 5. Personal Experiment 6. Enzymes Lab 7. The Importance of Water 8. Cell Membranes - How Do Small Materials Enter Cells? 9. Osmosis - Elodea Lab 10. Respiration - Yeast Lab 11. Cell Division - Egg Lab 12.

protein:ligand, K eq [protein:ligand] [protein][ligand] (1) can be restated as, K eq 1 [ligand] p 1 p 0 (2) where p 0 is the fraction of free protein and p 1, the fraction of protein binding the ligand. Assuming low protein concentration, one can imagine an isolated protein in a solution of Nindistinguishable ligands. Under these premises .

AP Biology Exam Review: DNA, Protein Synthesis & Biotechnology Helpful Videos and Animations: 1. Bozeman Biology: DNA Replication 2. Bozeman Biology: DNA and RNA - Part 1 3. Bozeman Biology: DNA and RNA - Part 2 4. Cold Spring Harbor Lab Animation: Griffith / Avery, McCarty, and Macleod Experiments 5. McGraw-Hill Animation: Hershey Chase Experiment

Biology 121: General Biology (w/Lab) Syllabus Bio K121, Four sem. hrs. credits Instructor: Kim Speight CRN#/Sec.: #10208/T1 & #10209/T1A email:kspeight@trcc.commnet.edu . The final exam must be taken to pass this course. LAB WRITE-UPS Lab write-ups will be due the week following completion of the lab. Pages from each lab packet will be

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