“Keystone Species, Shrinking Red Knots, and Biomes”

For your primary post, please respond to one of the following three topics with a post of at least 125 words that addresses each point given in the instructions. Also, please reply to at least one fellow student on any topic.

Topic 1

:  Keystone Species. Watch the video entitled “Some animals are more equal than others…” (1)* Then completely describe the concept of a keystone species, giving specific examples from the video.

Topic 2 [articles]: Shrinking Red Knots. Read two of the following three articles about shrinking Red Knots (2)*, (3)*, (4)*, or research additional information on your own. Then, address the following issues:

• (a) Explain how the lifecycle of the Red Knot depends on hatchlings emerging at the same time as the insects hatch.
• (b) What are the long-term ramifications of having a mismatch between the bird hatch and the insect hatch?
• (c) Of the two articles you read, which of them do you feel was most informative?  Why?

Topic 3 [research]: Biomes. The term “biome” is described in the textbook. For this topic, describe the biome where you grew up (or where you currently live). Identify your location, the biome of the region, and describe the major characteristics of that biome. Add enough detail and commentary from your own experience, so that your answer is 125 words or more. If you’re really ambitious, you could consider looking up the EPA “ecoregion,” which will give additional details about your region.

*References (in Strayer Writing Standards format).

1. HHMI Biointeractive, May 3, 2016, Some animals are more equal than others: keystone species and trophic cascades., https://www.youtube.com/watch?time_continue=1142&v=hRGg5it5FMI
2. Helen Briggs, May 13, 2016, Shrinking bird pays the bill for Arctic warming, http://www.bbc.com/news/science-environment-36266692
3. Joseph Dussault, May 12, 2016, Climate change chould be shrinking these arctic birds, http://www.csmonitor.com/Science/2016/0512/Climate-change-could-be-shrinking-these-Arctic-birds
4. Carl Zimmer, May 12, 2016, Climate change and the case of the shrinking red knots,  http://www.nytimes.com/2016/05/17/science/climate-change-bird-red-knots.html?_r=0

 

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How to Proceed

• Read through the introductory materials below.
• Open the Unit 5 Experiment Answer Sheet and complete the following Experiment exercises this unit:
  • Experiment 5 Exercise 1 – Transcription and Translation (~15 min)
  • Experiment 5 Exercise 2 – Translation and Mutations (~1 hr)
  • Experiment 5 Exercise 3 – Mutation Rates (~30 min)
• Save your completed Unit 5 Experiment Answer Sheet and submit it no later than Sunday midnight (CT).

Transcription and Translation – Introduction

Be sure that you have read over our online lecture this unit on DNA and read pp 177 to 181 in your book before starting. DNA can be a complex concept to grasp, and there is a lot of terminology to keep straight. These first two exercises will focus on transcription and translation, the two processes responsible for taking the information embedded in our DNA and using it to create a protein.

There are segments in our DNA called genes that code for the proteins needed to carry out cellular functions. These genes are a sequence of nucleotides; adenine (A), thymine (T), cytosine (C) and guanine (G) and the specific sequence of these nucleotides is what conveys the information needed to produce a given protein. In humans, the smallest gene is 252 nucleotides long, whereas the largest is more than 2 million nucleotides long! The genetic code is used to decipher the sequence of nucleotides into a sequence of amino acids. The code uses a series of three-nucleotide sequences called codons. Each different codon codes for an amino acid and it is this specific sequence of amino acids that determines what protein is formed.

DNA is found in our nucleus, yet our proteins are synthesized in the cytoplasm. A gene must first be transcribed into a form that can leave the nucleus. Transcription is the process in which a sequence of DNA used to synthesize a complementary strand of messenger RNA (mRNA). This mRNA acts a template and is used to translate the original DNA sequence into a protein, based on the information in its codons and the Genetic Code.

For example, the DNA sequence ATG-CGT-TAG-CGT-ATTC would be transcribed into the mRNA sequence UAC-GCA-AUC-GCA-UAA. Then, using Fig 10.11 on p 180 in your book, you can determine that this mRNA would be translated into the amino acid sequence Tyrosine-Alanine-Isoleucine-Alanine-Stop.

In Exercise 1, you will have the opportunity to demonstrate your understanding of transcription and translation. You will be using the following website; be sure that you are able to access and use the site:

University of Utah. No date. Transcription and Translation
https://learn.genetics.utah.edu/content/basics/transcribe/ (Links to an external site.)

In Exercise 2, you will apply what you learned in Exercise 1 and evaluate the effect that different types of mutations have on the outcome of transcription and translation. You’ll want to review these mutations on pp 186-187 of your book and in our online lecture on DNA before starting. You will be using the following website; be sure that you are able to access and use the site:

McGraw Hill. No date. Virtual Lab: DNA and Genes
http://glencoe.mheducation.com/sites/dl/free/0078802849/383936/BL_26.html (Links to an external site.)

Finally, in Exercise 3, you will complete a series of calculations to determine the probability of a mutation occurring within a gene that results in a change in protein structure. These are straight-forward math calculations; do not let them overwhelm you.

UNIT 5 EXPERIMENT ANSWER SHEET Please submit to the UNIT 5 Experiment SUBMISSION LINK no later than Sunday midnight.

SUMMARY OF ACTIVITIES FOR UNIT 1 EXPERIMENT ASSIGNMENT

· Experiment 5 Exercise 1 – Transcription and Translation

· Experiment 5 Exercise 2 – Translation and Mutations

· Experiment 5 Exercise 3 – Mutation Rates

 

Experiment 5 Exercise 1: Transcription and Translation

This exercise will ensure that you have a good understanding of the processes of transcription and translation. To get started, go to the following website:

University of Utah. No date. Transcription and Translation

http://learn.genetics.utah.edu/content/molecules/transcribe/

 

Procedure

A. Read over the information on the first screen and click on the click here to begin to proceed.

B. On the next screen transcribe the give DNA strand.

Table 1. Transcription of the DNA sequence (1.5 pts).

RNA

 

C. Once you have finished transcribing the DNA, you will then translate the RNA sequence. Follow the instructions on the screen.

Table 2. Translation (1.5 pts)

	Codon	Amino Acid
Codon 1
Codon 2
Codon 3
Codon 4
Codon 5
Codon 6

 

 

Experiment 5 Exercise 2: Translation and Mutations

Now that you know how to transcribe DNA and translate the mRNA message, let’s take a look at the different types of mutations that might disrupt this process. Review pp 186-187 in your book before beginning. In this exercise you will need to use the following website:

McGraw Hill. No date. Virtual Lab: DNA and Genes http://www.glencoe.com/sites/common_assets/advanced_placement/mader10e/virtual_labs_2K8/labs/BL_04/index.html

Read over the information in the Mutation Guide and close it when you are done. Note that there are several pages; you will need to click on Next to proceed through the Guide. If you want to review this material, you can click on the Mutation Guide button. You are going to run a series of simulations in which an mRNA sequence and its corresponding amino acid sequence is provided. You will be told what type of mutation you will you apply (= Mutation Rule) and you will have to determine the new, mutated mRNA and the resulting protein sequence.

Procedure

A. Click on the Mutate button to get started.

B. Find the Mutation Rule (lower left corner) and enter it into Table 3 below (see the Example provided).

C. Drag the appropriate nucleotides to build the new, Mutated mRNA sequence. If you make a mistake building the new mRNA sequence, drag the correct nucleotide and place it on top of the incorrect one (you cannot actually remove a nucleotide).

D. Once you have generated your Mutated mRNA sequence, you now need to build your Mutated amino acid sequence by matching the appropriate amino acid with each codon. Click on Genetic Code Chart to see the code or you can use Figure 10.11 on p 160 in your book.

NOTE: If you add a STOP codon, do NOT add any more amino acids after it!

 

E. Once you have finished, click on the Check button. If you are correct, then continue with Step F. If you had errors, you will have to Reset the simulation and start over with Step A. Here is what the results look like for the example provided:

F. When you have been successful, enter the Original mRNA sequence and the Original amino acid sequence in the Table below. Then enter the Mutated mRNA and Mutated protein sequence.

G. Click on Reset and repeat Steps A through F four more times so that you end up with FIVE replicates. Do not reuse the same Mutation Rule and do not use the rule used in the example (“the 4th A becomes a C”). If you get the same Mutation rule twice, Reset the simulation and run again.

Do NOT use the same Mutation rule as shown in the example and do NOT use the same Mutation Rule twice!

Table 3. Mutation rules, mRNA sequences and amino acid sequences (10 pts).

Rep	Mutation Rule and Sequences
E X A M P L E	Mutation rule: The 4th A becomes a C
	Original mRNA sequence	AUG CAC ACG GUG CGA GGG AGU CUG
	Original amino acid sequence	Met (Start) – His – Thr – Val – Arg – Gly – Ser – Leu
	Mutated mRNA sequence	AUG CAC ACG GUG CGC GGG AGU CUG
	Mutated amino acid sequence	Met (Start) – His – Thr – Val – Arg – Gly – Ser – Leu
	Consequence	Substitution appears to have had no effect; Arg Arg
1	Mutation rule:
	Original mRNA sequence
	Original amino acid sequence
	Mutated mRNA sequence
	Mutated amino acid sequence
	Consequence
2	Mutation rule:
	Original mRNA sequence
	Original amino acid sequence
	Mutated mRNA sequence
	Mutated amino acid sequence
	Consequence
3	Mutation rule:
	Original mRNA sequence
	Original amino acid sequence
	Mutated mRNA sequence
	Mutated amino acid sequence
	Consequence
4	Mutation rule:
	Original mRNA sequence
	Original amino acid sequence
	Mutated mRNA sequence
	Mutated amino acid sequence
	Consequence
5	Mutation rule:
	Original mRNA sequence
	Original amino acid sequence
	Mutated mRNA sequence
	Mutated amino acid sequence
	Consequence

 

Questions

1. What is a silent mutation? Did you see any examples of this in your mutations above? If so, which mutation rule(s) generated it? Cite your sources (2 pts).

 

2. What is a missense mutation and how does it differ from a nonsense mutation? Did you see examples of either of these types of mutation and if so, which mutation rule(s) generated it? Cite your sources (2 pts).

3. What is a frame-shift mutation and why are they so damaging? Did you see any examples of this in your mutations above? If so, which mutation rule(s) generated it? Cite your sources (2 pts).

 

4. Find a genetic disorder that develops as a result of one of the types of genetic mutations we have examined in this exercise. Identify the disorder and briefly describe the mutation responsible. Cite your sources (3 pts).

 

 

Experiment 5 Exercise 3: Mutation Rates

We learned in our second exercise that not all mutations have an observable effect. Yet the risk of a mutation being damaging is fairly significant, so it is important to understand the probability of them occurring. In this exercise, we are going to calculate the probability of a mutational event within a gene. You are given the necessary information below to complete the calculations. Do not let them overwhelm you; this is simple math, so think things through.

Assume that:

· there are approximately 3,000,000,000 base pairs in the mammalian genome (genes constitute only a small portion of this total)

· there are approximately 10,000 genes in the mammalian genome

· a single gene averages about 10,000 base pairs in size

 

Questions

1. Based on the assumptions above, in the mammalian genome, how many total base pairs are in all the mammalian genes? Show your math (2 pts).

2. What percentage (%) of the total genome does this represent? Show your math (2 pts).

 

3. What is the chance (%) that a random mutation will occur in any given gene? Show your math (2 pts).

 

4. Only 1 out of 3 mutations that occur in a gene result in a change to the protein structure. What is the probability that a random mutation will change the structure of a protein? Show your math (2 pts).

 

UNIT 1 Experiment Grading Rubric

Component	Expectation	Points
Experiment 5 Exercise 1	Demonstrates an understanding of the process of transcription and translation (Table 1 and 2).	3 pts
Experiment 5 Exercise 2	Correctly implements the proper mutation and transcribes the mRNA correctly (Table 3).	10 pts
	Demonstrates an understanding of the different types of mutations and their consequences (Questions 1-4).	9 pts
Experiment 5 Exercise 3	Correctly calculates the necessary information (Questions 1-4).	8 pts
TOTAL		30 pts

 

Updated April 2015

 

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