second notes

Isoleucine and Feedback Inhibition

• Isoleucine: An amino acid that is used up by cells.

• Active site: The region of an enzyme where substrate molecules bind and undergo a chemical reaction.

• Initial substrate:

  • Threonine is the initial substrate that enters the active site of the enzyme.

• Enzyme 1 (threonine deaminase): An enzyme that catalyzes the conversion of threonine into other metabolites.

• Feedback Inhibition:

  • The process by which the end product of a metabolic pathway inhibits an earlier step in the pathway, thus shutting down the pathway.

• Pathway progression:

  • After threonine is converted, it becomes Intermediate A, and subsequently follows other intermediates (B, C, D) through various enzymes until reaching the end product, which is Isoleucine.

  • Isoleucine binds to the allosteric site of Enzyme 2, preventing it from functioning, leading to the pathway's halt.

• Importance for cells:

  • Feedback inhibition is crucial for regulating metabolic pathways and maintaining homeostasis within the cell by preventing the overproduction of certain metabolites.

Localization of Enzymes Within Cell

• Mitochondrion:

  • Dimension: Approximately 0.5 μm.

  • Contains enzymes in its matrix involved in the second stage of cellular respiration.

  • Enzymes for the third stage of cellular respiration are embedded in the inner membrane.

Photosynthesis and Cellular Respiration

• Chemical Energy:

  • Found in food and is essential for life processes.

Big Ideas to Understand

• Photosynthesis:

  • Comprises of two main parts:

  • Light-dependent reactions: Capture light energy and generate ATP and NADPH.

  • Calvin Cycle: Uses ATP and NADPH to synthesize sugars.

• Cellular Respiration:

  • Encompasses three stages:

  • Glycolysis: Breakdown of glucose into pyruvate.

  • Citric Acid Cycle: Completes glucose breakdown to CO₂.

  • Oxidative Phosphorylation: Production of ATP via electron transport and chemiosmosis.

Autotrophic and Heterotrophic Nutrition

• Autotrophs:

  • Known as "self feeders". Examples include:

  • (a) Plants

  • (b) Cyanobacteria

  • (c) Multicellular alga

  • (d) Purple sulfur bacteria

  • (e) Unicellular protists

• Photoautotrophs: Organisms that utilize light to perform photosynthesis.

• Heterotrophs:

  • Referred to as "other feeders", rely on consuming organic compounds for nutrition.

Sources of Biomass

• Biomass composition: The living organisms (e.g., you, your pet, trees) are composed mainly of carbon-based biological molecules.

• Source of Carbon: The primary source of carbon for these organisms is carbon dioxide.

ATP Generation

• ATP Production:

  • Occurs through both photosynthesis and cellular respiration.

  • All organisms, including plants and animals, utilize ATP derived from organic molecules for energy utilization.

Photosynthesis Overview

• Photosynthesis: A fundamental anabolic process converting solar energy into chemical energy, specifically carbohydrates.

  • Overall Equation:
    $6 ext{CO}<em>2 + 12 ext{H}</em>2 ext{O} + ext{Light Energy} <br>ightarrow ext{C}<em>6 ext{H}</em>{12} ext{O}<em>6 + 6 ext{O}</em>2 + 6 ext{H}_2 ext{O}$

Two Stages of Photosynthesis

Light Reactions

• Processes that occur in the thylakoid membranes:

  • Water Splitting:

  • Water is split to provide electrons and protons, releasing O₂ as a by-product.

  • NADP+ Reduction:

  • Reduces NADP+ to NADPH.

  • ATP Generation:

  • Produces ATP from ADP.

The Calvin Cycle

• Uses ATP and NADPH produced in light reactions to convert CO₂ into carbohydrates.

  1. Carbon Fixation

  2. Reduction: Reduction of fixed carbon to carbohydrates using electrons from NADPH.

  3. Regeneration of CO₂ Acceptor: Prepares the cycle to start over.

Detailed Calvin Cycle Mechanism

• Three Phases:

  • Carbon Fixation: Involves the fixation of CO₂.

  • Reduction: Convert 3-phosphoglycerate into glyceraldehyde-3-phosphate (G3P).

  • Regeneration of RuBP: Recycles G3P to regenerate ribulose bisphosphate (RuBP).

• Overall Summary: Each set of 3 CO₂ entering the cycle yields 1 G3P.

Cellular Respiration Overview

• Cellular Respiration: A catabolic process releasing energy through the breakdown of complex molecules.

  • Overall Equation:
    $ext{C}<em>6 ext{H}</em>{12} ext{O}<em>6 + 6 ext{O}</em>2 <br>ightarrow 6 ext{CO}<em>2 + 6 ext{H}</em>2 ext{O} + ext{Energy (ATP + Heat)}$

Stages of Cellular Respiration

1. Glycolysis:

   • Sugar-splitting that breaks down glucose into two molecules of pyruvate. Occurs with or without oxygen.

2. Formation of Acetyl CoA:

   • Pyruvate is converted into acetyl CoA before entering the citric acid cycle.

3. Citric Acid Cycle:

   • Completes glucose breakdown to carbon dioxide.

   • Produces NADH and FADH2 for the electron transport chain.

Oxidative Phosphorylation

• Consists of two main components:

1. Electron Transport Chain: Carries and transfers electrons.

2. Chemiosmosis:

   • Protons are pumped across membranes, leading to ATP synthesis through ATP synthase.

• Energy Yield:

  • Maximum output can be around 30 to 32 ATP per glucose molecule.

Fermentation in Respiration

• Glycolysis can still proceed without oxygen through fermentation processes.

• Types of Fermentation:

  1. Alcohol Fermentation

  2. Lactic Acid Fermentation

Energy Flow and Chemical Recycling in Ecosystems

Energy Flow

• Light energy from the sun is converted into chemical energy by plants, then transferred through the food chain.

Chemical Cycling

• Chemical Recycling: Chemicals from the environment are incorporated into biological systems and then returned to the environment through processes such as decomposition by organisms like fungi and bacteria.