Biochemistry Chapter 4 Exercises

 

I. Concept Map

Objective:

Create a concept map to visualize your understanding of lipids. This activity evaluates your ability to integrate ideas from the provided reading and external knowledge, as well as your critical thinking.

Instructions:

1. Use black ink to include information directly from the provided reading.
2. Use red ink to write any questions or uncertainties you have about the topic.
3. Use blue ink to answer your question and/or add related information from other sources, experiences, or your own research.
4. Ensure all connections are clearly labeled, logical, and reflect thoughtful analysis.
5. Submit the concept map at the beginning of the the face-to-face class.

Evaluation Criteria:

• 10 points: All three colors used correctly and appropriately.
• 8 points: Two colors used correctly.
• 6 points: One color used correctly.
• 5 points: One color used incorrectly.
• 4 points: Two colors used incorrectly and/or the concept map is lacking.
• 3 points: All colors used incorrectly.
• 0 point: The concept map is not based on the reading selection.

Total Grade:

Midterm (30 points): 

Concept Map 1 = 10 points, Concept Map 2 = 10 points, Concept Map 3 = 10 points

Final Term (30 points):  

Concept Map 1 = 10 points, Concept Map 2 = 10 points, Concept Map 3 = 10 points

Passing  Grade per term: 18 points

II. Oral Discussion

Objective:

This activity aims to enhance your understanding of the biochemical principles related to nucleic acids and their relevance to agricultural applications. You will analyze real-world agricultural challenges, evaluate the role of these biochemical factors, and propose science-based solutions. This exercise fosters critical thinking, problem-solving, and practical application of biochemistry in agriculture.

Instructions:

1. Carefully read the case study provided to understand its context, challenges, and the biochemical factors (lipids) influencing agricultural practices..
2. Use the discussion questions to explore the role of organic water, pH, and buffers in the case study. Examine how these biochemical factors impact soil health, crop growth, and sustainable farming practices.
3. Identify how these biochemical principles are applied to address agricultural challenges. Evaluate both the positive and negative effects of the practices or technologies presented in the case study.
4. Apply key biochemical concepts such as buffer systems, acid-base balance, and the role of water as a solvent and reactant in biological processes. Relate these concepts to practical agricultural applications and challenges.
5. Work in your assigned groups to develop insights and solutions. Focus on how biochemical principles can optimize agricultural outcomes while considering environmental and economic impacts.
6. Three members will be randomly chosen to present your group’s findings, so ensure everyone is prepared to contribute. 

Evaluation Criteria:

1. Application of Biochemical Concepts (5 points):

   • Are biochemical concepts clearly identified and explained?
   • Does the group demonstrate a strong understanding of how these concepts apply to the case study and agricultural practices?

2. Relevance to Agricultural Applications (5 points):

   • Does the analysis address the agricultural challenges and opportunities highlighted in the case study?
   • Are the proposed solutions practical and informed by the biochemical principles discussed?

3. Critical and Environmental Analysis (5 points):

   • Does the response thoughtfully integrate environmental, social, and economic considerations into the evaluation of the case study?
   • Is there a balanced critique of the benefits, risks, and trade-offs associated with the practices or technologies analyzed?

Agriculture Students

Case Study 1: Genetically Modified Crops to Improve Drought Tolerance

Context:
Droughts threaten crop yield in many parts of the world. Scientists have used recombinant DNA technology to introduce drought-tolerance genes into maize and rice.

Biochemical Factors Involved:

• Nucleic acids (DNA) are modified to include genes that code for proteins regulating water retention and stress response.
• Water as a solvent plays a key role in the enzymatic reactions during gene expression.
• Soil pH and buffer systems influence nutrient availability for genetically modified crops.

Challenges:

• Potential loss of crop biodiversity.
• Public perception of GMOs.

Discussion Questions:

• How does altering nucleic acids contribute to improved drought tolerance?
• How do soil pH and buffer systems influence the uptake of water and nutrients in these GM crops?
• What are the environmental and social implications of using GMO seeds in drought-prone areas?

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Case Study 2: CRISPR-Cas9 for Disease Resistance in Cassava

Context:
Cassava mosaic virus affects food security in developing countries. CRISPR-Cas9 technology edits cassava DNA to resist this virus.

Biochemical Factors Involved:

• DNA editing targets specific nucleic acid sequences to remove or alter susceptibility genes.
• Water and pH impact enzymatic activity required for successful gene editing in plant cells.

Challenges:

• Regulatory hurdles in approving CRISPR-edited crops.
• Potential off-target genetic effects.

Discussion Questions:

• How does CRISPR-Cas9 use nucleic acid recognition to enhance disease resistance?
• What role does cellular pH and buffers play in facilitating CRISPR-based modifications?
• What trade-offs exist between crop security and natural genetic diversity?

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Case Study 3: RNA Interference (RNAi) to Control Insect Pests in Cotton

Context:
Insect pests damage cotton crops. RNAi technology silences genes in pests by feeding them plants containing double-stranded RNA sequences that match insect genes.

Biochemical Factors Involved:

• RNA molecules are used to block specific gene expressions in target pests.
• Water as a transport medium for RNAi molecules in plants.
• Soil buffers maintaining plant health and RNA uptake.

Challenges:

• Insect resistance development over time.
• Ecosystem disruption.

Discussion Questions:

• How do nucleic acids (RNAi) help control pest populations in cotton farming?
• How might soil pH and water balance affect the delivery of RNA molecules within the plant?
• What are the possible ecological consequences of pest population suppression using RNAi?

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Case Study 4: DNA-Based Soil Microbiome Monitoring for Sustainable Fertilization

Context:
Soil health is influenced by microbial diversity. Farmers now use DNA sequencing to monitor soil microbes and adjust fertilizer use accordingly.

Biochemical Factors Involved:

• Soil DNA analysis reveals microbial populations critical to nitrogen fixation and nutrient cycling.
• Soil pH and buffers influence microbial DNA stability and enzymatic processes.

Challenges:

• Cost and accessibility of soil DNA testing for small farmers.
• Risk of overreliance on technology without farmer training.

Discussion Questions:

• How is DNA analysis used to inform sustainable fertilizer practices?
• How do pH and buffers in soil affect microbial DNA stability and community structure?
• What are the economic and environmental trade-offs of using DNA-based soil monitoring?

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Case Study 5: DNA Fingerprinting for Plant Variety Protection in Rice Farming

Context:
Plant breeders develop new rice varieties and protect their work through DNA fingerprinting to confirm genetic identity.

Biochemical Factors Involved:

• Nucleic acids (DNA profiles) are used to distinguish plant varieties.
• Soil and water conditions influence gene expression and phenotypic traits.

Challenges:

• Intellectual property disputes between breeders and farmers.
• Ethical concerns over patenting seeds.

Discussion Questions:

• How is nucleic acid analysis applied in plant variety protection?
• How might soil water content and pH affect the expression of desirable traits in these varieties?
• What are the implications of seed patenting on agricultural communities?

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Case Study 6: Development of DNA Vaccines for Livestock in Integrated Farming Systems

Context:
Farmers are using DNA vaccines to protect poultry and livestock from viral diseases, ensuring healthy animals and higher productivity.

Biochemical Factors Involved:

• Synthetic DNA sequences are introduced to stimulate immune responses in livestock.
• Animal feed and water buffers ensure the stability of DNA vaccine components.

Challenges:

• Cold-chain requirements for DNA vaccine storage.
• Ethical concerns in animal biotechnology.

Discussion Questions:

• How are nucleic acids used in developing vaccines for agricultural livestock?
• What role do water pH and buffer solutions play in the stability and delivery of DNA vaccines?
• How can small-scale farmers sustainably integrate DNA vaccination into their practices?

III. Online Quiz

Objective:

This activity aims to assess your understanding of key biochemistry concepts, including biomolecular interactions, metabolic pathways, and their application to real-world scenarios, particularly in agriculture and sustainable practices.

Instructions:

Access the quiz through the provided link and answer all questions thoroughly before the deadline. Ensure your responses demonstrate a clear application of biochemistry principles, focusing on the molecular, physiological, and environmental implications in the scenarios presented. Late submissions will not be accepted, so complete the quiz on time.

LINK: ONLINE QUIZ 4 (not yet live)

Deadline: (to be announced)

IV. Public YouTube Video Group 3 & 4

Objective:

To create an engaging 5–8 minute YouTube video that demonstrates your understanding of a scientific study related to the current Biochemistry topic, highlighting its application in agriculture. This exercise aims to evaluate your ability to analyze and connect biochemical principles to practical agricultural solutions while producing a professional, concise, and creative presentation.

Instructions:

Two groups will produce a video showcasing their understanding of a scientific study related to the current Biochemistry topic, highlighting its application in agriculture. The videos will be graded based on editing skills (smooth transitions, clear audio, and proper pacing), content (accurate integration of case study details and critiques), and videography (lighting, composition, camera work, and professional appearance). Once completed, upload your video publicly to YouTube and submit the link as a comment under the designated photo in our private Facebook group. Ensure your work aligns with the provided rubric and maintains a clear, engaging delivery.

Group leaders not assigned to produce a video for the week will give a peer grade for the video of the any of the groups assigned to produce a video. This will serve as their attendance/grade. Only 2 groups are allowed to peer grade a video. Groups leaders can only grade a group once. 

Total Grade:

Midterm (50 points): 

Video 1 = 30 points; Peer Grade 1 = 10 points; Peer Grade 2 = 10 points

Final Term(50 points): 

Video 2 = 30 points; Peer Grade 1 = 10 points; Peer Grade 2 = 10 points

Passing Grade per term: 30 points

V. Speech Group 5 & 6

Objective:

The objective of this activity is to develop your ability to analyze and effectively communicate how nucleic acids are relevant in agricultural practice. This task challenges you to craft a TED Talk-style presentation that incorporates insights from class discussions and clearly connects your assigned case study to real-world agricultural applications. Your presentation should demonstrate a strong understanding of biochemistry principles and their relevance to sustainable farming and agricultural productivity.

Instructions:

Only members of two groups mentioned above will prepare a 250-word speech based on the how nucleic acids influence agricultural practices. The speech must integrate all corrections from the oral discussion and adhere to writing mechanics: include a title, your complete name, section, date, group, proper margins, and indentation. Have your manuscript reviewed and checked by your group leader before submitting it in our next face-to-face class. Record your speech  in TED Talk style as a video, ensuring clear delivery, and post the video in the designated album in our private Facebook group. Evaluation will focus on writing mechanics (10 points), content quality (based on the rubric below), and delivery skills (rubric provided).

Students who are not assigned to deliver a speech for the week are expected to give a peer grade by commenting on their post. Only 2 peer grade is allowed per speech. You can only peer grade a classmate once.