Biochemistry Chapter 1 Introduction, Water, pH and Buffers

The Importance of Biochemistry in Agriculture

Biochemistry is the study of the chemical processes in living things. In agriculture, biochemistry is very important because it helps us understand how plants grow, how to make them stronger, and how to produce more food. Here are some key reasons why biochemistry matters in agricultural sciences:

1. Understanding Plant Growth

Biochemistry helps us learn how plants use sunlight, water, and nutrients from the soil to grow. By studying these processes, we can find ways to help plants grow better and faster. For example, knowing how photosynthesis works allows us to improve farming practices.

Example: Advances in understanding photosynthesis have led to the development of "C4 rice." Researchers modify rice plants to use C4 photosynthesis (common in plants like maize) instead of the less efficient C3 pathway. This innovation allows rice to grow faster and use water more efficiently, helping farmers in drought-prone regions.

2. Making Plants Stronger

Plants face many challenges like drought (lack of water), pests (bugs that harm plants), and diseases. Biochemists study how plants respond to these challenges at a chemical level. This knowledge helps scientists develop new varieties of crops that can survive tough conditions, ensuring farmers have reliable harvests.

Example: Genetic engineering has produced crops like Bt cotton, which contains a gene from the bacterium Bacillus thuringiensis. This gene helps the plant produce a natural pesticide against bollworm pests, reducing crop losses and decreasing reliance on synthetic pesticides.

3. Improving Soil Health

Healthy soil is essential for growing crops. Biochemistry helps us understand the nutrients in the soil and how they affect plant growth. By learning about soil chemistry, farmers can use fertilizers more effectively and practice sustainable farming that keeps the soil healthy for future generations.

Example: Studies on nitrogen-fixing bacteria, like Rhizobium, have improved the use of biofertilizers in legume crops such as soybeans and peanuts. By enhancing these bacteria's ability to convert atmospheric nitrogen into a form plants can use, farmers can reduce the need for synthetic nitrogen fertilizers.

4. Creating Natural Fertilizers and Pesticides

Using chemical fertilizers and pesticides can harm the environment. Biochemists work on creating natural fertilizers (biofertilizers) and natural pest control methods (biopesticides). These products help plants grow while being safer for the environment.

Example: The production of Neem-based biopesticides utilizes the active compounds in neem leaves and seeds. These biopesticides protect crops from pests like aphids and caterpillars while being environmentally friendly and biodegradable.

5. Ensuring Food Security

As the world’s population grows, we need more food. Biochemistry helps increase food production by improving crop yields and developing crops that have more nutrients. This is important for feeding everyone and reducing hunger.

Example: Golden rice, a genetically modified variety, contains higher levels of beta-carotene, a precursor of vitamin A. This crop helps combat vitamin A deficiency in populations dependent on rice as a staple food, particularly in Southeast Asia and Africa.

6. Reducing Food Waste

After crops are harvested, they can spoil quickly. Biochemistry helps us understand how fruits and vegetables ripen and decay. By knowing these processes, we can find ways to keep food fresh longer, which reduces waste and ensures that more food reaches people.

Example: Research on ethylene, the plant hormone responsible for ripening, has led to the development of products like ethylene inhibitors (e.g., 1-MCP or 1-methylcyclopropene). These inhibitors delay ripening in fruits like bananas and apples, extending their shelf life and reducing food spoilage during transport.

Biochemistry is crucial in agriculture because it helps us understand how plants grow, make them stronger against challenges, improve soil health, create safer farming products, ensure enough food for everyone, and reduce waste after harvesting. By applying biochemistry in agriculture, we can build a better future for farmers and consumers alike.

The Chemical Composition of Living Organisms and Its Relevance to Biological Processes

Living organisms are made up of various chemical compounds that are essential for life. Understanding these compounds helps us grasp how biological processes work. Here’s a simple breakdown of the chemical composition of living things and why it matters.

1. Key Elements in Living Organisms

The most important elements found in living organisms include:

• Carbon (C): The backbone of all organic molecules.
• Hydrogen (H): Found in water and organic compounds.
• Oxygen (O): Essential for respiration and found in water.
• Nitrogen (N): A key component of proteins and nucleic acids.
• Phosphorus (P): Important for energy transfer and DNA structure.
• Sulfur (S): Found in some amino acids and vitamins.

These elements combine to form the four main types of biochemical compounds: carbohydrates, proteins, lipids, and nucleic acids.

2. Major Biochemical Compounds

Each type of biochemical compound has unique structures and functions:

• Carbohydrates: Made of sugar molecules (monosaccharides). They provide energy for cells and are important for plant structure (like cellulose in cell walls).
• Proteins: Composed of amino acids. They perform many functions, including building tissues, transporting molecules, and speeding up chemical reactions as enzymes.
• Lipids: Includes fats and oils. They store energy, make up cell membranes, and act as signaling molecules.
• Nucleic Acids: DNA and RNA are made from nucleotides. They store genetic information and help in protein synthesis.

3. Importance of Chemical Composition

Understanding the chemical composition of living organisms is crucial for several reasons:

1. Biological Processes: All life processes, like digestion, respiration, and growth, involve chemical reactions. For example, when we eat food, our bodies break down carbohydrates into glucose for energy through a series of chemical reactions.
2. Cell Structure: The arrangement of these biochemical compounds determines the structure and function of cells. For instance, the lipid bilayer forms the cell membrane, which protects the cell and controls what enters or leaves.
3. Metabolism: Biochemical compounds are involved in metabolism—the set of life-sustaining chemical reactions. Enzymes (which are proteins) help speed up these reactions, making it possible for cells to convert food into energy efficiently.

Living organisms are composed mainly of carbon-based compounds that play critical roles in biological processes. By understanding the chemical composition—such as carbohydrates for energy, proteins for structure and function, lipids for storage and membranes, and nucleic acids for genetic information—we can better appreciate how life works at a molecular level. This knowledge is fundamental for fields like medicine, agriculture, and environmental science.

Properties of Water and Its Role in Maintaining Biochemical Stability

Water is essential for all living organisms, including plants, animals, and soil. Its unique properties make it crucial for maintaining biochemical stability. Let’s explore the key properties of water and how they contribute to the stability of life.

1. Polar Nature of Water

Water molecules are polar, meaning they have a slight positive charge on one side (the hydrogen atoms) and a slight negative charge on the other side (the oxygen atom). This polarity allows water to form hydrogen bonds with other water molecules and with different substances. The polarity of water helps it dissolve many substances, making it an excellent solvent. This property is vital for transporting nutrients in plants and animals.

Example: In plants, the polarity of water enables it to dissolve minerals and nutrients in the soil, creating a nutrient-rich solution absorbed by roots. In the human body, water's solvent properties allow nutrients like glucose and amino acids to travel through the bloodstream to cells.

Water dissolve minerals and nutrients in the soil.

2. Cohesion and Adhesion

Water molecules stick to each other (cohesion) and to other materials (adhesion). 

Cohesion: This property allows water to form droplets and creates surface tension, which enables small insects to walk on water. Surface tension caused by cohesion allows insects like water striders to walk on water without sinking.

Adhesion: Water can climb up plant stems through tiny tubes called xylem due to adhesion. This movement is essential for transporting water from the roots to the leaves. Capillary action, a combination of cohesion and adhesion, allows water to move upward through the narrow xylem vessels in tall trees like redwoods, providing hydration to leaves far above the ground.

3. High Specific Heat Capacity

Water has a high specific heat capacity, meaning it can absorb a lot of heat without changing temperature significantly. This property helps regulate temperature in living organisms and their environments. For example, it allows aquatic environments to remain stable, providing a suitable habitat for fish and other organisms.

Example: Coastal areas often have milder climates compared to inland regions because large bodies of water, like oceans, absorb and release heat slowly. Similarly, organisms like fish thrive in stable aquatic environments where temperature fluctuations are minimal due to water's high specific heat capacity.

4. High Heat of Vaporization

It takes a lot of energy to convert water from liquid to vapor (evaporation). When organisms sweat or when water evaporates from plant leaves, it cools the surface. This cooling effect is crucial for temperature regulation in both plants and animals.

Example: When humans sweat during exercise, the evaporation of water from the skin surface cools the body, helping maintain a stable internal temperature. In plants, the process of transpiration (evaporation of water from leaf surfaces) prevents overheating in hot climates.

Transpiration prevents overheating in hot climates

5. Density and Ice Formation

Water is unique because it is less dense as a solid (ice) than as a liquid. Ice floats on water. This property insulates bodies of water in cold weather, allowing aquatic life to survive beneath the ice layer.

Example: During winter, ice forms on the surface of ponds and lakes while the water below remains liquid, providing a stable habitat for fish and other aquatic organisms. The insulating ice layer prevents the entire body of water from freezing, protecting ecosystems

6. Role in Biochemical Reactions

Water is involved in many chemical reactions in living organisms, including hydrolysis (breaking down molecules) and dehydration synthesis (building larger molecules). These reactions are essential for metabolism, growth, and energy production in all living things.

Example:

• Hydrolysis: In digestion, water breaks down complex carbohydrates like starch into simpler sugars such as glucose, which cells can use for energy.
• Dehydration synthesis: Plants use this reaction to build cellulose, the structural component of their cell walls, from glucose molecules

The properties of water—its polarity, cohesion, adhesion, high specific heat capacity, high heat of vaporization, density as ice, and its role in biochemical reactions—are fundamental to maintaining biochemical stability in plants, animals, and soils. Without these properties, life as we know it would not be possible. Water supports nutrient transport, temperature regulation, and various chemical processes that are critical for survival.

Understanding pH and Buffer Systems

What is pH?

pH is a way to measure how acidic or basic a solution is. It tells us about the concentration of hydrogen ions (H⁺) in a solution. Here’s how it works:

Acidic solutions have a lot of hydrogen ions and have a pH less than 7.

Neutral solutions, like pure water, have a pH of 7.

Basic (or alkaline) solutions have fewer hydrogen ions and have a pH greater than 7.

Watch from start to finish

The pH Scale

The pH scale ranges from 0 to 14:

- 0 to 6: Acidic (like lemon juice or vinegar)

- 7: Neutral (like pure water)

- 8 to 14: Basic (like baking soda)

Each step on the scale represents a tenfold change in acidity or basicity. For example, a solution with a pH of 5 is ten times more acidic than one with a pH of 6.

Why is pH Important?

In our bodies, many processes depend on the right pH. For example:

Enzymes, which are proteins that help speed up chemical reactions, often work best at specific pH levels.

Our blood has a very narrow pH range (around 7.35 to 7.45). If it gets too acidic or too basic, it can cause serious health problems.

What are Buffer Systems?

A buffer system is a solution that helps maintain a stable pH when small amounts of acids or bases are added. Buffers are crucial in biological systems because they keep our body fluids at the right pH.

Watch this video until 2:32

How Do Buffers Work?

Buffers are usually made of two components:

1. A weak acid: This can donate H⁺ ions when needed.

2. A weak conjugate base: This can accept H⁺ ions when there are too many in the solution.

When you add an acid (which increases H⁺) or a base (which decreases H⁺) to a buffer solution, the weak acid and weak base work together to keep the pH stable.

Example of a Buffer System

One common buffer system in our body is the bicarbonate buffer system:

- When there’s too much acid (more H⁺), bicarbonate (HCO₃⁻) can react with H⁺ to form carbonic acid (H₂CO₃), reducing acidity.

- When there’s too little acid (too basic), carbonic acid can break down into bicarbonate and release H⁺ to lower the pH.

Summary

To summarize:

• pH measures how acidic or basic a solution is.
• Buffers help maintain stable pH levels in our bodies by using weak acids and bases.

Understanding these concepts is essential for studying biochemistry and how living organisms function. If you have any questions or need clarification on anything, feel free to ask!

pH, Buffers, and Their Importance in Agriculture

Today, we will discuss how pH and buffer systems relate to agriculture. Understanding how pH and buffer systems relate to agriculture is essential for growing healthy crops and using agricultural chemicals effectively.

Why is pH Important in Agriculture?

1. Nutrient Availability: The pH level influences which nutrients are available to plants. For example, iron becomes less available in alkaline (high pH) soils, which can lead to deficiencies. In calcareous soils, common in regions like Central Luzon, Philippines, the soil tends to be alkaline due to high calcium carbonate content. This high pH reduces the availability of iron, leading to iron chlorosis in crops like rice and mangoes. Affected plants show yellowing leaves due to insufficient chlorophyll production. Farmers often address this by applying iron chelates or acidifying fertilizers to lower the soil pH.

   

   In calcareous soils, the soil tends to be alkaline due to high calcium carbonate content. This high pH reduces the availability of iron, leading to iron chlorosis in crops like rice and mangoes.

   
   
2. Microbial Activity: Soil microbes help break down organic matter and make nutrients available to plants. These microbes thrive best at specific pH levels, usually around neutral to slightly acidic. In acidic soils found in tropical rainforests, decomposition of organic matter is slow because beneficial microbes like nitrifying bacteria (e.g., Nitrosomonas and Nitrobacter) cannot thrive. This leads to poor nitrogen cycling, limiting nitrogen availability to plants. To improve microbial activity, farmers may apply lime to raise the pH closer to neutral, enhancing microbial decomposition and nutrient availability.
3. Pesticide Effectiveness: The effectiveness of pesticides can change with pH. Many pesticides work better in acidic conditions. If the water used for mixing pesticides has a high pH, the pesticides can break down quickly and become less effective. In pineapple plantations in Mindanao, the effectiveness of the herbicide glyphosate can decrease if mixed with alkaline water from local sources. Glyphosate degrades faster in high pH water, reducing its ability to control weeds. To mitigate this, farmers add buffering agents to the spray mixture to maintain an acidic pH, ensuring the herbicide remains effective.

Agricultural Applications of pH and Buffers

1. Soil Management: Farmers often test soil pH to determine if it needs adjusting. If the soil is too acidic, they might add lime (which is basic) to raise the pH. If it’s too basic, they might use sulfur or organic matter to lower it.

Example: In the Benguet highlands of the Philippines, farmers growing strawberries often deal with acidic soils due to continuous fertilizer use and high rainfall. To correct this, they apply agricultural lime (calcium carbonate) to raise the pH, creating a more neutral environment that supports nutrient availability and healthy plant growth. Conversely, in areas with alkaline soils, such as parts of Pampanga, farmers apply elemental sulfur or compost to lower the pH, making nutrients like iron and manganese more accessible to crops like rice and vegetables.

2. Water Quality for Irrigation: Farmers need to monitor the pH of their irrigation water. If it's too high, they can use buffering agents to bring it down to an optimal level for crop growth and pesticide effectiveness.

Example: In Nueva Ecija, a major rice-producing region, irrigation water can sometimes become alkaline due to high bicarbonate levels in groundwater. To prevent reduced nutrient uptake and pesticide inefficiency, farmers use acidifiers like phosphoric acid to lower the pH of irrigation water, ensuring optimal conditions for rice growth and improving the effectiveness of agrochemicals.

3. Compatibility of Chemicals: Some agricultural chemicals work best at specific pH levels. For example, phosphate buffers can help maintain the right pH when mixing pesticides, ensuring they remain effective and do not break down prematurely.

Example: In banana plantations in Davao, fungicides like mancozeb are used to control fungal diseases. However, mancozeb is unstable in alkaline water and breaks down rapidly, reducing its effectiveness. To solve this, farmers add phosphate buffer solutions to their spray tanks, stabilizing the pH and ensuring the fungicide remains effective throughout application.

4. Enhancing Nutrient Uptake: By using organic acids as buffers, farmers can improve the uptake of nutrients by plants while reducing harm to plant tissues[1]. This also helps in making micronutrients more available in the soil.

Example: In tomato farms in Bukidnon, growers use humic and fulvic acids (organic acids) to improve nutrient absorption, especially micronutrients like iron and zinc. These organic acids lower the soil pH in localized zones around the root system, making nutrients more soluble and accessible to the plants, leading to healthier growth and higher yields.

Understanding pH and buffer systems is crucial for successful agriculture:

• The right pH ensures that plants can absorb nutrients effectively.
• Buffers help maintain stable conditions in both soil and water.
• Adjusting pH can enhance pesticide effectiveness and promote healthy plant growth.

References

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