BIOL 110

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1 TAKE HOME EXAM FOR THE MOLECULAR GENETICS REVIEW BIOL 110 To understand microbiology, it is essential to have a fairly good understanding of such basic points of molecular genetics (proteins, enzymes, DNA, RNA, transcription, translation, and mutation. The purpose of this take home exam is to enable you – or force you if you prefer – to review these topics that you learned in your prerequisite course, BIOL 110. It will also introduce you to mechanisms of genetic recombination in bacteria. Read the Review of Molecular Genetics for Take Home Exam included in your hard copy of my Lecture Guide. It can be found at the end of Part-1 of my BIOL 230 Lecture E-text following the Unit 3 segment. I would urge you to use the hard copy of this material in conjunction with the illustrations and animations in the online version found on my web page at http://faculty.ccbcmd.edu/courses/bio141/lecguide/takehome/index.html After you read these sections and study the illustrations and animations, answer the enclosed Take Home Exam. OBJECTIVES FOR TAKE HOME EXAM FOR THE MOLECULAR GENETICS (DO NOT ANSWER THESE.) While you don’t have to turn in the Objectives listed below, these are objectives I would expect you to be fairly fluent with before we get very far into this course. (This is the major reason why BIOL 110 is a prerequisite for Microbiology.) If you answer the objectives first, you will find it easier to answer the take home exam. I. MICROBIAL GENETICS A. Polypeptides, Proteins, and Enzymes 1. Define or describe the following: a. amino acid b. “R” group c. peptide bond d. peptide e. polypeptide f. primary protein structure g. secondary protein structure h. tertiary protein structure i. quaternary protein structure j. gene 2. Describe how the primary structure of a protein or polypeptide ultimately detemines its final three-dimensional shape. 3. Describe how the order of nucleotide bases in DNA ultimately determines the final three-dimensional shape of a protein or polypeptide. B. Deoxyribonucleic Acid 1. State the 3 basic parts of a deoxyribonucleotide. 2. State which nitrogenous bases are purines and which are pyrimidines. 3. Define complementary base pairing. 2 C. DNA Replication 1. Briefly describe the process of DNA replication in bacteria. D. Ribonucleic Acid 1. State the 3 basic parts of a ribonucleotide. 2. State 3 ways RNA differs from DNA. 3. State the function of each of the following: a. tRNA b. mRNA c. rRNA E. Polypeptide and Protein Synthes 1. Define the following: a. gene b. transcription c. translation 2. Briefly describe the function of the following in terms of bacterial protein synthesis: a. mRNA b. RNA polymerase c. promoter region d. codon e. 30S ribosomal subunit f. 50S ribosomal subunit g. tRNA h. anticodon i. P-site of ribosome j. A-site of ribosome k. peptidyl transferase l. nonsense (stop) codon 3. Describe how the order of nucleotide bases along a gene in the DNA ultimately determines the three dimensional shape of the protein coded for by that gene. F. Mutation 1. Define mutation and genetic recombination. 2. Describe 2 different mechanisms of mutation and, in terms of protein synthesis, describe the 4 possible results that may occur as a result of these mutations. G. Genetic Recombination in Bacteria 1. Briefly describe the following means of genetic recombination in bacteria: a. transformation b. transduction c. conjugation 3 BIOL 230 MICROBIOLOGY TAKE HOME EXAM FOR THE MOLECULAR GENETICS REVIEW Name: Lab Section: 60 points 1. Matching _____ The molecule synthesized by complementary base pairing of RNA nucleotides with DNA nucleotides to match a portion of one strand of DNA coding for a protein or polypeptide. _____ The enzymes that initiate and terminate transcription as well as join RNA nucleotides together. _____ A specific nucleotide sequence at the beginning of a gene to which RNA polymerase binds to start transcription. _____ A series of 3 consecutive mRNA bases coding for one specific amino acid. _____ The molecules that picks up specific amino acids and carries those amino acids to the ribosomes during translation. _____ A series of 3 tRNA bases complementary to a specific codon. _____ The site on a 50S ribosomal subunit to which new charged tRNA molecules first attach. _____ A series of 3 mRNA bases coding for no amino acid; serves as a signal to terminate translation. _____ The molecules that, along with proteins, form ribosomes. A. anticodon G. “P” site of ribosome B. “A” site of ribosome H. promoter region C. codon I. rRNA D. DNA polymerase J. RNA polymerases E. mRNA K. tRNA F. nonsense (stop) codon 4 2. Matching _____ The order of amino acids in a protein. _____ The folded, three-dimensional, functional shape of a protein. _____ Metabolic reactions in which molecules are broken down. _____ The sequence of purine and pyrimidine bases on one strand of DNA that codes for the amino acid sequence of a particular protein or polypeptide. _____ The process wherein mRNA is synthesized to be complementary to a gene. _____ The process wherein tRNA carries specific amino acids to the ribosomes and inserts them in proper place according to the mRNA “message.” A. gene F. anabolic reactions B. nucleotide G. catabolic reactions C. primary protein structure H. transcription D. secondary protein structure I. transformation E. tertiary protein structure J. translation 3. _____ The nitrogenous bases cytosine and thymine are: A. purines B. codons C. proteins D. complementary to each other E. pyrimidines 4. _____ Complementary base pairing is the hydrogen bonding of: A. adenine with thymine; cytosine with guanine B. adenine with guanine; thymine with cytosine C. adenine with cytosine; guanine with uracil D. adenine with guanine; thymine with uracil E. Mo with Larry; Curly with Sven the Wonder Llama 5. _____ Which does NOT describe transcription? A. RNA polymerase B. mRNA synthesis occurs C. tRNA carries amino acids to the ribosomes D. copying of a portion of one strand of DNA E. complementary base pairing 6. _____ In RNA, uracil hydrogen bands with: A. guanine B. cytosine C. thymine D. adenine E. Throckmorton the Mediocre Moose (whose second cousin, by coincidence, is Sven the Wonder Llama) 5 7. _____ Which does NOT describe an R-plasmid? A. usually has genes for coding for a sex pilus B. has genes for multiple antibiotic resistance C. usually allows for conjugation D. found in many gram-negative bacteria E. carried from one bacterium to another by temperate phages 8. _____ Which describes a DNA nucleotide? A. 1 nitrogenous base, 1 phosphate, 1 ribose B. 1 nitrogenous base, 1 protein, 1 ATP C. 1 deoxyribose, 1 codon, 1 phosphate D. 1 nitrogenous base, 1 deoxyribose, 1 phosphate E. faster than a speeding bullet, more powerful than a locomotive, able to leap a Wonder Llama, eg, Sven, in a single bound 9. _____In the primary structure of a protein, the amino acids are connected to one another by: A. hydrogen bonds B. disulfide bonds C. congealed Yoo Hoo brand chocolate drink D. RNA E. peptide bonds 10. _____ ______________ molecules of tRNA with one or more attached amino acids can bind to a single ribosome at one time. A. one B. two C. three D. four E. 376,251,134.628, + or – pi (which, by one of those strange quirks of fate, just happens to be the telephone number of Olga, booking agent and personal manager to Sven, the Wonderous Wonder Llama – not available for birthdays) 11. _____ During protein synthesis, the proper amino acid is put in the proper place according to the genetic message by: A. transcription B. an anticodon hydrogen bonding with a codon C. RNA polymerase D. a nonsense codon E. bet you thought I was going to say “Sven” of Wonder Llama fame 12. _____ The sequence of _________________ in a DNA molecule ultimately determines the order of amino acids in proteins. A. deoxyribose molecules B. purine and pyrimidine bases C. phosphates D. anticodons E. plasmids 6 13. _____ Addition and deletion mutations usually result in: A. one wrong amino acid in protein B. what happens when the dental technician X-rays your teeth after always leaving the room and giving you flimsy excuses for doing so like “I have to go put my socks in the dryer” or “I think my Wonder Llama just threw up a hairball” C. a reading frame shift D. one wrong codon in the DNA E. substitution of one base in the DNA 14. _____A tRNA with an ACC anticodon will hydrogen bond with a ______ mRNA codon. (Use your codon sheet, Fig. 8 in the transcription section; Fig. 2 in the translation section.) A. TGG B. UGG C. ACC D. UCC E. stop 15. _____ A tRNA with an ACC anticodon will insert the amino acid ________ during translation. (Use your codon sheet, Fig. 8 in the transcription section; Fig. 2 in the translation section.) A. Cys B. Ser C. Trp D. Arg E. Svn DISCUSSION 1. Briefly DESCRIBE THE FUNCTION of the following in terms of bacterial protein synthesis: (2 points each) A. mRNA B. codon C. tRNA D. anticodon E. nonsense codon 7 2. As a result of a substitution mutation, a DNA base triplet 3’ ATA 5’ is charged to 3’ ATT 5’. State specifically what effect this would have on the resulting protein. (Use your codon sheet, Fig. 8 in the transcription section; Fig. 2 in the translation section.) (4 points) 3. Describe 2 different mechanisms of mutation and, in terms of protein synthesis, describe the 4 possible results that may occur as a result of these mechanisms. (7 points) 4. DESCRIBE how the order of nucleotide bases along a gene in the DNA ultimately determines the threedimensional shape and function of the protein coded for by that gene. (5 points) 5. Describe R-plasmid conjugation and its significance to medical microbiology. (3 points) 6. Compare transformation and transduction in bacteria. (2 points)

 
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UMUC Biology 102 103 Lab 5: Meiosis

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Your Full Name:

 

UMUC Biology 102/103

Lab 5: Meiosis

INSTRUCTIONS:

 

·         On your own and without assistance, complete this Lab 5Answer Sheet electronically and submit it via the Assignments Folder by the date listed intheCourse Schedule (under Syllabus).

·         To conduct your laboratory exercises, use the Laboratory Manual located under Course Content. Read the introduction and the directions for each exercise/experiment carefully before completing the exercises/experiments and answering the questions.

·         Save your Lab 5Answer Sheet in the following format:  LastName_Lab5 (e.g., Smith_Lab5).

·         You should submit your document as a Word (.doc or .docx) or Rich Text Format (.rtf) file for best compatibility.

 

Pre-Lab Questions

 

  1. Compare and contrast mitosis and meiosis.

 

 

  1.  What major event occurs during interphase?

 

 

Experiment 1: Following Chromosomal DNA Movement through Meiosis

In this experiment, you will model the movement of the chromosomes through meiosis I and II to create gametes.

concept_tab_l

Materials

2 Sets of Different Colored Pop-it® Beads (32 of each – these may be any color)

8 5-Holed Pop-it® Beads (used as centromeres)

    
   

 

Procedure:

Part 1: Modeling Meiosis without Crossing Over

As prophase I begins, the replicated chromosomes coil and condense…

  1. Build a pair of replicated, homologous chromosomes. 10 beads should be used to create each individual sister chromatid (20 beads per chromosome pair). Two five-holed beads represent each centromere. To do this…
Figure 3: Bead set-up. The blue beads represent one pair of sister chromatids and the black beads represent a second pair of sister chromatids. The black and blue pair are homologous.
Figure 3: Bead set-up. The blue beads represent one pair of sister chromatids and the black beads represent a second pair of sister chromatids. The black and blue pair are homologous.
    1. Start with 20 beads of the same color to create your first sister chromatid pair. Five beads must be snapped together for each of the four different strands. Two strands create the first chromatid, and two strands create the second chromatid with a 5-holed bead at the center of each chromatid.  This creates an “I” shape.
    2. Connect the “I” shaped sister chromatids by the 5-holed beads to create  an “X” shape.
    3. Repeat this process using 20 new beads (of a different color) to create the second sister chromatid pair.
  2. Assemble a second pair of replicated sister chromatids; this time using 12 beads, instead of 20, per pair (six beads per each complete sister chromatid strand).
  3. Pair up the homologous chromosome pairs created in Step 1 and 2. DO NOT SIMULATE CROSSING OVER IN THIS TRIAL. You will simulate crossing over in Part 2.
  4. Configure the chromosomes as they would appear in each of the stages of meiotic division (prophase I and II, metaphase I and II, anaphase I and II, telophase I and II, and cytokinesis).
  5. Diagram the corresponding images for each stage in the sections titled “Trial 1 – Meiotic Division Beads Diagram”. Be sure to indicate the number of chromosomes present in each phase.
Figure 4: Second set of replicated chromosomes.
Figure 4: Second set of replicated chromosomes.
  1. Disassemble the beads used in Part 1. You will need to recycle these beads for a second meiosis trial in Steps 8 – 13.

Part 1 – Meiotic Division Beads Diagram

Prophase I

 

Metaphase I

 

Anaphase I

 

Telophase I

 

Prophase II

 

Metaphase II

Anaphase II

 

Telophase II

 

Cytokinesis

Part 2: Modeling Meiosis with Crossing Over

  1. Build a pair of replicated, homologous chromosomes. 10 beads should be used to create each individual sister chromatid (20 beads per chromosome pair). Two five-holed beads represent each centromere. To do this…
    1. a. Start with 20 beads of the same color to create your first sister chromatid pair. Five beads must be snapped together for each of the four different strands. Two strands create the first chromatid, and two strands create the second chromatid with a 5-holed bead at the center of each chromatid.  This creates an “I” shape.
    2. Connect the “I” shaped sister chromatids by the 5-holed beads to create  an “X” shape.
    3. Repeat this process using 20 new beads (of a different color) to create the second sister chromatid pair.
  2. Assemble a second pair of replicated sister chromatids; this time using 12 beads, instead of 20, per pair (six beads per each complete sister chromatid strand). Snap each of the four pieces into a new five-holed bead to complete the set up.
  3. Pair up the homologous chromosomes created in Step 8 and 9.
  4. SIMULATE CROSSING OVER. To do this, bring the two homologous pairs of sister chromatids together (creating the chiasma) and exchange an equal number of beads between the two. This will result in chromatids of the same original length, there will now be new combinations of chromatid colors.
  5. Configure the chromosomes as they would appear in each of the stages of meiotic division (prophase I and II, metaphase I and II, anaphase I and II, telophase I and II, and cytokinesis).
  6. Diagram the corresponding images for each stage in the section titled “Trial 2 – Meiotic Division Beads Diagram”. Be sure to indicate the number of chromosomes present in each cell for each phase. Also, indicate how the crossing over affected the genetic content in the gametes from Part1 versus Part 2.

Part 2 –  Meiotic Division Beads Diagram:

Prophase I

 

Metaphase I

 

Anaphase I

 

Telophase I

 

Prophase II

 

Metaphase II

 

Anaphase II

 

Telophase II

 

Cytokinesis

 

 

Post-Lab Questions

1.      What is the ploidy of the DNA at the end of meiosis I? What about at the end of meiosis II?

 

2.      How are meiosis I and meiosis II different?

 

3.      Why do you use non-sister chromatids to demonstrate crossing over?

 

4.      What combinations of alleles could result from a crossover between BD and bd chromosomes?

 

 

 

5.      How many chromosomes were present when meiosis I started?

 

6.      How many nuclei are present at the end of meiosis II? How many chromosomes are in each?

 

7.      Identify two ways that meiosis contributes to genetic recombination.

 

8.      Why is it necessary to reduce the number of chromosomes in gametes, but not in other cells?

 

9.      Blue whales have 44 chromosomes in every cell. Determine how many chromosomes you would expect to find in the following:

 

Sperm Cell:

Egg Cell:

Daughter Cell from Mitosis:

Daughter Cell from Meiosis II:

 

10.  Research and find a disease that is caused by chromosomal mutations. When does the mutation occur? What chromosomes are affected? What are the consequences?

 

11.  Diagram what would happen if sexual reproduction took place for four generations using diploid (2n) cells.

 

 

Experiment 2: The Importance of Cell Cycle Control

Some environmental factors can cause genetic mutations which result in a lack of proper cell cycle control (mitosis). When this happens, the possibility for uncontrolled cell growth occurs. In some instances, uncontrolled growth can lead to tumors, which are often associated with cancer, or other biological diseases.

In this experiment, you will review some of the karyotypic differences which can be observed when comparing normal, controlled cell growth and abnormal, uncontrolled cell growth. A karyotype is an image of the complete set of diploid chromosomes in a single cell.

 

 

 

 

concept_tab_lProcedure

Materials

*Computer Access

*Internet Access

  

*You Must Provide

 

 

 

  1. Begin by constructing a hypothesis to explain what differences you might observe when comparing the karyotypes of human cells which experience normal cell cycle control versus cancerous cells (which experience abnormal, or a lack of, cell cycle control). Record your hypothesis in Post-Lab Question 1.

    Note: Be sure to include what you expect to observe, and why you think you will observe these features. Think about what you know about cancerous cell growth to help construct this information

  2. Go online to find some images of abnormal karyotypes, and normal karyotypes. The best results will come from search terms such as “abnormal karyotype”, “HeLa cells”, “normal karyotype”, “abnormal chromosomes”, etc. Be sure to use dependable resources which have been peer-reviewed
  3. Identify at least five abnormalities in the abnormal images. Then, list and draw each image in the Data section at the end of this experiment. Do these abnormalities agree with your original hypothesis?

Hint: It may be helpful to count the number of chromosomes, count the number of pairs, compare the sizes of homologous chromosomes, look for any missing or additional genetic markers/flags, etc.

Data

 

 

 

 

 

Post-Lab Questions

1.      Record your hypothesis from Step 1 in the Procedure section here.

 

 

2.      What do your results indicate about cell cycle control?

 

 

3.      Suppose a person developed a mutation in a somatic cell which diminishes the performance of the body’s natural cell cycle control proteins. This mutation resulted in cancer, but was effectively treated with a cocktail of cancer-fighting techniques. Is it possible for this person’s future children to inherit this cancer-causing mutation? Be specific when you explain why or why not.

 

 

4.      Why do cells which lack cell cycle control exhibit karyotypes which look physically different than cells with normal cell cycle.

 

 

5.      What are HeLa cells? Why are HeLa cells appropriate for this experiment?

 

 

 
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Application: Inheritance Lab

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A-Plus Writer, would it be possible for you to complete the attached lab report for the assignment listed below? Please?

Application: Inheritance Lab

Have you noticed any similarities among you and your parents or other relatives? Even if you do not know your biological parents, you can guess some of their physical characteristics based on your own physical characteristics or phenotypes. You can do this by applying Mendelian genetics.

For your Application Assignment, complete the Inheritance Lab in which you identify your phenotypes for several physical characteristics such as the presence of dimples or a widow’s peak. Then, infer your possible genotypes, as well as your parents’ possible genotypes.

To prepare for this Application Assignment:

Consider what Mendelian genetics is and how you can determine genotypes based on phenotypes and vice versa.

Review the Inheritance Lab Background document (see attachment), focusing on the phenotypes you observe for the Inheritance Lab and how to identify genotypes associated with those phenotypes.

Review the lab instructions in the Inheritance Lab Report (see attached), focusing on the steps you must follow and the information you must complete in the report. You may complete this report by hand as you complete the lab; however, by Day 7, you submit an electronic version of this document for your Application Assignment.

NOTE: You do not need to purchase any materials to complete this lab.

The Assignment:

Complete the Inheritance Lab Report

© 2012 Laureate Education, Inc.

Inheritance Lab Background Background on Mendelian Genetics When traits are the result of a single gene with a few distinct alleles, you may use the logic of Mendelian genetics to predict the genotypes of offspring. To apply Mendelian genetics, you must understand the following terms: genotype, phenotype, dominant allele, recessive allele, heterozygous, homozygous, and Punnett square. Here is an example of a Punnett square. In this example, we will assume that having freckles is a simple single allele example of Mendelian genetics and that the dominant allele is freckles (F) and the recessive allele is no freckles (f). A heterozygous parent with a genotype of Ff mates with a homozygous parent who has an ff genotype. This is an example:

f f F Ff Ff f ff ff

Based on what you know about Mendelian genetics, what percentage of the offspring in the Punnett square above will display freckles? You may also use Mendelian genetics to infer possible genotypes of parents based on the phenotype of a child. For example, if a child displays freckles, what are his or her possible genotypes? (Hint: There are two possible genotypes.) Based on this answer, what genotypes might the parents have? (Hint: There are more than two possible genotypes for the parents.) Continuing with the above example, imagine that you do not know your birth parents and have no siblings, but that you do have freckles. Thus, your phenotype is F, but what is your genotype? Both an FF and an Ff individual would display freckles, so your genotype could be either of these. Using Mendelian genetics, you can infer the different possible pairings of parental phenotypes that would lead to your genotypes. For instance, let’s examine the case in which you are a heterozygote for freckles and consider what possible parental crosses could have resulted in the Ff genotype. Any of the following parental crosses are possible:

FF x Ff FF x ff Ff x Ff

Does this make sense? If not, run a Punnett square on each cross. (See pages 157–158 in your course text for how to use a Punnett square. You may also practice using a Punnett square by referring to the Punnett square calculator listed in the Optional Resources section.) You can also predict which of the above crosses would be most likely by considering which of these pairings is most likely to give an Ff offspring (e.g., 25%, 50%, or 100% probability). You will use this logic by identifying several particular phenotypes and then infer your parents’ possible genotypes.

 

 

© 2012 Laureate Education, Inc.

BACKGROUND ON PHENOTYPES For this lab, you will identify your phenotype for a variety of physical characteristics, and infer your possible genotypes based on the phenotype. Then you will infer possible genotypes for each of your parents. Save the Inheritance Lab Report document to your computer so you may complete an electronic version of the report. You submit this to your Instructor for your Application Assignment for this week. The following are the phenotypes you will identify in the lab report. When identifying the possible genotypes, use the letters listed below for the dominant and recessive alleles. EARLOBES Having free earlobes is a dominant trait (E); having attached earlobes is a recessive trait (e). Explanation: A free earlobe hangs below the point where the ear attaches to the head. An attached earlobe attaches directly to the side of the head.

DIMPLES Having dimples is a dominant trait (D); not having dimples is recessive (d). Explanation: Dimples are natural indentations in the face on either side of the mouth. (A person may have just one dimple on one side of the mouth.)

 

 

© 2012 Laureate Education, Inc.

TONGUE ROLLING The ability to roll up the sides of the tongue is dominant (T); not having the ability to roll up the sides of the tongue is recessive (t).

 

 

 

© 2012 Laureate Education, Inc.

TOE LENGTH ON FOOT Having a second toe longer than the foot’s big toe is a dominant trait (F); having a second toe shorter than the foot’s big toe is a recessive trait (f). Explanation: The second toe in the above statement refers to the toe that is adjacent (next to) the big toe on your foot. If the second toe is longer than the big toe, you have the dominant trait; if the second toe is shorter than the big toe, you have the recessive trait.

WIDOW’S PEAK Having a distinct point in the hairline at the top of the face is a dominant trait (W); not having a distinct point in the hairline at the top of the face is a recessive trait (w).

 
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BIO – Exercise 2: The Globin Gene

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Exercise 2: The Globin Gene
Procedure

1. Complete the DNA molecule by writing a complementary strand.

Coding Strand: CGT CTC TTC GGA CAC Complementary Strand:
2. Write the mRNA sequence that will be created in the process of transcription. The DNA coding strand has the information for the gene, so the strand must be transcribed. The relationships are slightly different for RNA, because RNA does not have T; therefore, U should be substituted for T. To transcribe DNA to RNA, the pairing relationship is A – U, T – A, C – G, and G – C, respectively.

Coding Strand: CGT CTC TTC GGA CAC

mRNA Strand:

3. Translate the mRNA into amino acids. Use Table 1 as a reference. Remember, when a “stop”
codon is recognized, the protein creation is terminated.

mRNA Strand:
Amino Acids Formed:

Questions

A. How many nucleotides would it take to construct the mRNA coding strand of the β-subunit of the hemoglobin A molecule?
B. How many nucleotides would it take to model the entire β-subunit of the hemoglobin A molecule?
C. Is the β-subunit of the hemoglobin A molecule a complete DNA molecule (chromosome) or part of one? Explain.
D. What would happen if one of the DNA nucleotides was deleted? What if the first T was substituted for an A? Would a substitution always result in a change? Explain why or why not.
E. Using your newly formed model of DNA from Exercise 1, write the coding strand below. Use the coding strand to determine the mRNA strand and the amino acids formed. Do this separately for Row 1 and Row 2 of your DNA model.

Data Table: Newly Formed Model of DNA from Exercise 1
ROW 1 ROW 2
Coding Strand
mRNA Strand
Amino Acids Formed
F. Did the new DNA model form any two of the same amino acids?
G. Optional: Compare the amino acids that were formed in this experiment with those of classmates who also performed this experiment. Were there many similarities?

 
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