Principles of Biology

Description

Lab 8 Molecular genetics of the color mutations in the rock pocket mice instructions

Purpose: The purpose of this lab is to practice reading the genetic code of a coat color gene Mc1r and transcribing the gene into a transcript of messenger RNA and translating the transcript using the genetic codon table provided into protein. There are two versions of the same gene in rock pocket mice: version 1 – a wild-type Mc1r gene present in the population, and version 2 – a mutated Mc1r gene, also present in the population which results in change of the mouse coat color when the mutated gene is expressed.  This lab allows practice of transcription and translation by reading the gene sequences provided in the lab and identifying differences and types of mutations present in Mc1r mutant.

Students may complete this work as team of two only with explanation of the contribution of each student.

Advice from your instructor: I have changed the gene sequence for Mc1r wild –type and mutated genes so I strongly suggest you do not plagiarize. Plagiarized work will result in 0 grade and the report may not be revised.

 

Learning outcomes:

• Understand the function of Mc1r gene in rock pocket mice
• Know the genus and species name of commonly called rock pocket mice
• Explain how and why the mutation of coat color in these mice helps their survival
• Name the two pigments which cause coat color in rock pocket mice
• Explain three types of mutations in genes
• Explain the results of three types of genetic mutations when expressed as protein

 

INTRODUCTION   

THE ROCK POCKET MOUSE

The rock pocket mouse, Chaetodipus intermedius, is a small, nocturnal animal found in the deserts of the southwestern United States. Most rock pocket mice have a sandy, light-colored coat that enables them to blend in with the light color of the desert rocks and sand on which they live. However, populations of primarily dark-colored rock pocket mice have been found living in areas where the ground is covered in a dark rock called basalt caused by geologic lava flows thousands of years ago. Refer to Figure 1 below. Scientists have collected data from a population of primarily dark-colored mice living in an area of basalt called the Pinacate lava flow in Arizona, as well as from a nearby light-colored population. Researchers analyzed the data from these two populations in search of the genetic mutation responsible for the dark coat color. Their analyses led to the discovery of a mutation in the Mc1r gene that is involved in coat-color determination.

 

Figure 1. Dark and light coat color rock pocket mice

Molecular Ecology (2003)  12 , 1185–1194. Different genes underlie adaptive melanism in different populations of rock pocket mice HE HOEKSTRA and MW NACHMAN Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA

THE MC1R GENE

Two pigments primarily determine the coat color of rock pocket mice: eumelanin, which is dark-colored, and pheomelanin, which is light-colored. The products of several genes, including Mc1r gene, control the synthesis of these pigments. Mc1r gene encodes a protein, the melanocortin 1 receptor (MC1R), that is embedded in the cell membranes of melanocytes, specialized pigment-producing skin cells. The melanocytes of wild-type (non-mutant) mice produce more pheomelanin than eumelanin. The result is a sandy- colored mouse. The mutated version of the Mc1r gene, however, triggers melanocytes to increase the production of eumelanin, resulting in the dark coat-color phenotype.

 

GENE MUTATION

A gene mutation is any change in the DNA sequence of a gene from its original sequence. Gene mutations may change the structure of the resulting protein. A change in protein structure can change, negate, or have no effect on the protein’s function. There are several types of genetic mutations, and they may affect the expressed product of protein if present in the gene. Below identifies types of mutations found in genes and the potential effects of mutation on the gene’s expressed protein when the gene is transcribed and translated.

Types of mutations

1. Substitution mutation

Replacement of one nucleotide of DNA for another.

Mutations that affect a single nucleotide are called “point mutations”

1. Insertion mutation

Addition of one or more nucleotide(s) to the DNA gene sequence

Insertion of nucleotide(s) can result in “frame-shift” mutation

• Deletion mutation

Loss of one or more nucleotide(s) from the DNA gene sequence

Deletion of nucleotide(s) can result in “frame-shift” mutation

 

Potential effects a gene mutation when expressed as protein

1. Silent mutation

This mutation does not cause a change in the amino acid sequence of the protein; therefore, there is NO change in the resulting protein

 

1. Missense mutation

This mutation causes an amino acid in the sequence to be changed to different amino acid. This type of mutation causes a change in the primary structure of the protein (the linear sequence of amino acids), which may result in a change in the protein’s three-dimensional shape

 

• Nonsense mutation

This mutation causes the protein to be truncated (cut short) due to the incorporation of a “stop” signal into the DNA sequence

This results in translation being stopped before the amino acid sequence of the protein has been fully translated

 

MATERIALS

• Genetic code chart (page 6 of instructions)
• Wild-type and mutant version Mc1r genes given in instructions pages
• Blue, red, and green font colors or highlighter provided in Microsoft Word to use to identify mutations in the mutated Mc1r gene. Please note mutations do not exist in the wild-type Mc1r gene so do not change the font color or use highlighter in the wild-type gene.
  • Blueidentifies silent mutation
  • Greenidentifies nonsense mutation
  • Redidentifies missense mutation
  • See procedure step 5 below for use of these colors to identify genetic mutations

 

PROCEDURE

1. View video:

Watch the video in D2L Module 9, Making of the fittest before completing this lab: https://www.youtube.com/watch?v=sjeSEngKGrg&feature=youtu.be

2. Transcribe each Mc1r gene wild-type and mutant into RNA:

Use the DNA nucleotide sequences for the wild-type and mutant genes in the Table I to write the complementary mRNA sequence for the portion of Mc1r gene given. (Note: You are only transcribing short portions of the DNA sequence for this protein. The actual gene contains 954 base pairs.)

Here is an example of writing the messenger RNA complementary to a DNA gene (mRNA):

DNA gene X                                                  AGT AAC  CTT  GAC

Transcript mRNA complementary to DNA  UCA UUG GAA CUG

 

3. Translate the mRNA into amino acids:

Using the genetic codon table on page 6 to translate the mRNA sequence completed in step 2 into MC1R protein (Note: You are translating only a portion of protein. The full protein is 317 amino acids long. The numbers above the columns in the tables indicate amino acid positions in the protein sequence.)

 

4. Identify the type of mutation in the Table 2 mutant Mc1r gene:

This identification applies only to Table 2 mutant Mc1r gene and do not apply to Table 1 wild type Mc1r gene. Using the information in materials above to determine whether each of the substitution mutation results in a silent, missense, or nonsense mutation for the gene where it occurred.

Using the Table 2 mutant Mc1r gene data:

• Write the DNA, mRNA, and amino acid using Blue text for silent mutations
• Write the DNA, mRNA, and amino acid using Red text for missense mutations
• Write the DNA, mRNA and amino acids using Green text for nonsense mutations

 

5. Complete report by answering follow-up questions:

Answer the follow-up questions after completion of filling in Tables 1 and 2. These answers are to be your own and should not be copied from another source. If you need to reference a source then paraphrase the information (do not use direct quotes) from this source and write the source you obtained this information from. Use of plagiarism in the report will result in a 0 grade for the lab report. The idea for your own work is to read information and then rephrase what has been learned in your own words as you understand these ideas so that you gain practice in reading, interpretation, and presentation of the work of others.

 

6. Upload completed report to Assignment Lab 8 in D2L:

Submit the completed Lab 8 report to Assignment Lab 8 by October 20, 11PM. If working as student team of two then include each student’s name and work contributed by each student in the report.  Grading will be based on accuracy and completeness of answers.

 

 

 

 

GENE TABLE 1: WILD-TYPE MC1R GENE (PHENOTYPE LIGHT COAT-COLOR)

                                    Amino acid 154                                                                                                                                                                                                                                                                                                                         161

DNA	TAC	TGC	CCC	TGA	CGA	GGA	ATA	GAG
mRNA
Amino Acid

                                                                           Amino acid  209                                                                                                                                                                                                                                                                                                                                                                                            212

DNA	ACA	CAG	GAA	GAC
mRNA
Amino Acid

          Amino acid       230                                                                                                                                                                                                                                   238

DNA	AAG	ACA	GAC	TGT	CCA	CAG	GCC	AGA	TTG
mRNA
Amino Acid

 

GENE TABLE 2: MUTANT MC1R GENE (PHENOTYPE DARK COAT-COLOR)

                                    Amino acid 154                                                                                                                                                                                                                            161

DNA	TAC	TAC	CCG	TGA	CGA	GGT	ATA	GAC
mRNA
Amino Acid

   

                                                                              Amino acid  209                                                                                                                                                                                                                                                                                                                                         212

DNA	ACA	GAG	AAA	GAC
mRNA
Amino Acid

      

        Amino acid 230                                                                                                                                                238

DNA	ATG	ACA	GAC	TGT	CCA	GAG	GGC	AGA	TAG
mRNA
Amino acid

 

GENETIC CODE CHART

 

The standard genetic table containing mRNA codons and its translated amino acid. See circular version of this table below. The innermost circle represents the first letter of the codon followed by the second middle ring for the second letter and the third outermost ring for the third letter. Find the corresponding amino acid in the outer circle.

Image credit: “The genetic code,” by OpenStax College, Biology (CC BY 3.0).

 

Questions to answer after completion of Tables 1 and 2:

1. Identify the function of the protein expressed by the Mc1r gene in rock pocket mice.
2. Name the mouse genus and species commonly called rock pocket mice (use proper spelling and capitalization)
3. Identify the pigments that cause the coat color of rock pocket mice
4. Explain how genetic mutations in the rock pocket mouse coat color benefitted this species.
5. Explain the general effect of a silent mutation in a protein’s amino acid sequence.
6. Refer to Table 2 and identify one silent mutation that occurred in MC1R protein mutant by writing the amino acid position it occurred at. Here is an example of what I am looking for: A silent mutation of LEU to LEU occurred at amino acid position 016.
7. Explain the general effect of a missense mutation in a protein’s amino acid primary sequence. Explain whether the mutant amino acid sequence would or would not be the same as the wild-type amino acid sequence with this type of mutation.
8. Refer to Table 2 and identify one missense mutation that occurred in MC1R protein mutant by writing the amino acid position it occurred at. Here is an example of what I am looking for: A missense mutation of PHE to MET occurred at amino acid position 020.
9. Name the structure used by all cells to translate messenger RNA (mRNA) into a protein.
10. Analyze this hypothetical cell condition: A mutant cell is no longer able to express ribosomal RNA and ribosomal proteins needed to produce the small subunit of ribosome. Is this mutant cell able to synthesize proteins? Explain your answer.