10/9

Welcome and Introduction

• Greeting to the class and welcoming students.

• Session due to flooding on October 9.

SI Sessions

• SI (Supplemental Instruction) sessions are available with Anna and Autumn.

• Recommend attending as they are tied directly to the class material, offering an opportunity for deeper understanding and practice in a collaborative setting.

Announcements

• Marine Biology Student Colloquium on October 10.

  • Location: DNR Auditorium, 217 Fort Johnson Road, James Island.

  • Transportation is required; no shuttle provided.

  • QR code provided for further information regarding speakers and topics.

• Research matchmaking session scheduled for October 21, designed to connect students with potential research opportunities and faculty mentors.

• Reminder of posted midterm grades.

• Midterm grades compile performance from quizzes, exams, and task grades.

  • The lowest quiz grade will be dropped at semester's end to account for a potential poor performance or absence.

• Importance of midterm grades:

  • A grade lower than a C (e.g., D or F) often indicates a high likelihood (approximately 70% chance) of persistence of that grade or lower by the semester’s end.

  • An F at midterm may significantly impact the final grade, making a C or lower highly probable without significant intervention.

• Advice to communicate concerns regarding grades:

  • Discussion with the instructor is highly recommended to explore academic strategies and potential improvements.

  • Consultation with the academic success and retention office is also recommended for comprehensive support.

Academic Resources

• Academic Success and Retention Office offers assistance with GPA calculation, understanding academic standing, and connecting students with relevant support services.

• Center for Student Learning provides various resources including strategies for effective note-taking (e.g., Cornell, outlining), active studying techniques (e.g., spaced repetition, practice problems), and individualized academic coaching to improve learning skills and performance.

Assignment Instructions

• Upcoming assignment: Drawing and presenting part of cellular respiration. This likely involves illustrating a specific stage (e.g., glycolysis, Citric Acid Cycle) and explaining its key steps, inputs, and outputs.

• Clarification about assignment percentages within the overall course grade structure.

• Office hours planned for later in the day from 3 to 4 PM for individual student support and questions.

Future Classes

• Instructor planning to teach Bio $112$ in Spring $2026$. Recommendations to consult academic advisers as majors differ in requirements, ensuring students register for appropriate core and elective courses.

Cellular Respiration Overview

• Discussion resumes on coenzyme electron carriers from Chapter 8.2.

• Coenzymes overview:

  • FAD (Flavin adenine dinucleotide) is reduced to FADH₂: accepts two electrons and two protons ($H^+$) during redox reactions, specifically in the Citric Acid Cycle.

  • NAD⁺ (Nicotinamide adenine dinucleotide) is reduced to NADH: grabs electrons and a hydrogen ion ($H^+$) during catabolic redox reactions, carrying high-energy electrons to the electron transport chain.

  • NADP⁺ (Nicotinamide adenine dinucleotide phosphate) involved in photosynthesis, reduced to NADPH: carries electrons for anabolic reactions, particularly in the Calvin cycle.

Energy Transformations

• Overview of energy transformations in living organisms, specifically through photosynthesis and cellular respiration, which are complementary processes.

  • Photosynthetic organisms (autotrophs) transform light energy (kinetic electromagnetic energy) into chemical bond energy (potential energy) stored within the C-H bonds of carbohydrates (e.g., glucose) through an endergonic process.

  • All organisms (autotrophs and heterotrophs) then metabolize carbohydrates, breaking down these high-energy bonds in an exergonic process, transforming the stored potential energy into a more readily usable form: ATP (adenosine triphosphate), which also represents potential energy stored in its phosphate bonds.

  • This transformation process can be summarized as a flow of energy:

    • Kinetic (light energy) $<br>ightarrow$ Potential (chemical bonds in carbohydrates) $<br>ightarrow$ Potential (chemical bonds in ATP) $<br>ightarrow$ Kinetic energy (used to power various cellular functions like muscle contraction, active transport, and biosynthesis).

Photosynthesis Reaction

• Photosynthesis is characterized as an endergonic reaction because it requires a net input of energy, specifically light energy, to proceed.

  • Reactants: Low-energy molecules, carbon dioxide ($6CO<em>2$) and water ($6H</em>2O$).

  • Needs energy input (kinetic energy from sunlight) to synthesize high-energy organic molecules.

  • Products: High-potential energy carbohydrates ($C<em>6H</em>{12}O<em>6$) and oxygen ($6O</em>2$) as a byproduct. The energy from sunlight is captured and stored in the chemical bonds of glucose.

Characteristics of Cellular Respiration

• Overview of cellular respiration as an exergonic reaction: A metabolic pathway that releases rather than consumes energy, proceeding spontaneously.

  • Involves breaking down complex, high-potential energy carbohydrates (like glucose) into simpler molecules, requiring oxygen (aerobic respiration).

  • Byproducts: Low-energy molecules, carbon dioxide ($6CO<em>2$) and water ($6H</em>2O$).

  • A significant portion of the released energy is captured and used to synthesize ATP, but some energy is inevitably released as heat, illustrating the second law of thermodynamics (increase in entropy).

  • Energy transformations display: reactants (glucose) with higher potential energy $<br>ightarrow$ products ($CO<em>2$, $H</em>2O$) with lower potential energy; the total energy transformation is exergonic, meaning riangle G < 0 (negative change in Gibbs free energy).

Stages of Cellular Respiration

1. Glycolysis:

   • Takes place exclusively in the cytosol (cytoplasm) of the cell, making it an anaerobic process (does not require oxygen).

   • Glucose (a 6-carbon sugar) is broken down into two molecules of pyruvate (each with 3 carbons).

   • Involves an initial energy investment phase, using $2$ ATP molecules, followed by an energy payoff phase.

   • Net yield per glucose molecule: $2$ ATP (via substrate-level phosphorylation) and $2$ NADH.

   • NAD⁺ is oxidized to NADH during this phase, carrying electrons for later steps.

2. Pyruvate Processing (Oxidation):

   • Occurs in the mitochondrial matrix in eukaryotes (or cytoplasm in prokaryotes).

   • Converts each pyruvate (3 carbons) from glycolysis to acetyl CoA (2 carbons) by decarboxylation (release of one $CO_2$ molecule per pyruvate).

   • Reduces more NAD⁺ to NADH ($1$ NADH per pyruvate, so $2$ NADH per glucose).

   • The remaining $2$-carbon acetyl group combines with coenzyme A to form acetyl CoA.

3. Citric Acid Cycle (Krebs Cycle / TCA Cycle):

   • Occurs in the mitochondrial matrix.

   • Oxidation of each acetyl CoA into two molecules of $CO_2$. This completes the breakdown of the original glucose molecule.

   • For each acetyl CoA entering the cycle (two per glucose), multiple electron carriers are reduced: $3$ NAD⁺ are reduced to NADH and $1$ FAD is reduced to FADH₂.

   • One ATP (or GTP, which is then converted to ATP) is also generated per cycle via substrate-level phosphorylation.

4. Electron Transport Chain (ETC) and Oxidative Phosphorylation:

   • Takes place in the inner mitochondrial membrane.

   • NADH and FADH₂ donate their high-energy electrons to a series of protein complexes (the ETC).

   • As electrons move down the ETC, energy is released and used to pump protons ($H^+$) from the mitochondrial matrix into the intermembrane space, creating a proton gradient.

   • This proton gradient powers ATP synthase (chemiosmosis), an enzyme that uses the flow of $H^+$ back into the matrix to generate a large amount of ATP from ADP and inorganic phosphate ($P_i$).

   • Oxygen acts as the final electron acceptor at the end of the ETC, forming water ($H_2O$).

   • This stage is responsible for generating the vast majority of ATP (approximately $26-28$ ATP per glucose) through aerobic respiration.

Glycolysis Detailed Look

• Glycolysis starts the oxidation of glucose; it splits the 6-carbon glucose molecule into two 3-carbon pyruvate molecules.

• Energy Investment Phase requires ATP:

  • Step 1: Phosphorylation of glucose to glucose-$-6$-phosphate by hexokinase, using $1$ ATP. This traps glucose inside the cell and makes it more reactive.

  • Step 3: Phosphorylation of fructose-$-6$-phosphate to fructose-$-1,6$-bisphosphate by phosphofructokinase, using another $1$ ATP. This is a crucial irreversible step.

• Enzyme catalyzing key steps, especially phosphofructokinase, regulates the pathway, ensuring glycolysis proceeds when ATP levels are low and slows down when ATP is abundant.

Key Takeaway from Glycolysis

• Phosphofructokinase acts as a crucial regulatory point of glycolysis. It is an allosteric enzyme that is inhibited by high levels of ATP (which signals sufficient energy) and citrate (an intermediate of the Citric Acid Cycle), and activated by high levels of AMP (signaling low energy). This link ATP availability to pathway activation and overall cellular energy demands.

Wrap Up

• Class interruptions due to Zoom issues; attempts at interaction through polling.

• Reminders about the importance of understanding metabolic pathways (exergonic vs. endergonic reactions) for overall biological function and energy flow.

• Encouraged attending additional sessions and checking notifications during breaks for important updates or additional resources.