Exam II Review - Spring 2026

Exam II Review Notes

Instructor: Sam Nutile, Ph.D.
Course: Penn State Behrend
Term: Spring 2026

Life Requires Energy

  • Second Law of Thermodynamics

    • States that entropy in a system will increase until thermodynamic equilibrium is reached.

  • Entropy

    • Definition: A measure of disorder in a system.

    • Notion: The universe is tending towards disorder.

  • Order and Life

    • Life requires order, which raises the question:

    • How does life create order from disorder?

    • Answer: Life creates order by using energy.

Coupling Reactions

  • Spontaneous Reactions

    • Definition: Reactions that proceed with a negative change in Gibbs free energy (–ΔG).

  • Types of Reactions

    • Reduction-Oxidation Reactions: Involving the transfer of electrons.

    • Reactions involving Light: Energy harnessed from sunlight.

    • Bond Breaking: Critical in energy transformations.

Nitrogen

  • Element Symbol: N

  • Atomic Number: 7

  • Atomic Mass: 14.007 amu

ATP (Adenosine Triphosphate)

  • Structure:

    • Consists of adenine, ribose, and three phosphate groups linked by phosphoanhydride bonds.


    • ATP Structure

  • Energy Sources:

    • ATP can derive energy from sunlight or from food consumption.

  • Energy Available:

  • The Gibbs free energy change (–ΔG°) indicates energy available for cellular work and chemical synthesis.

Respiration

  • General Equation:

    • [CH₂O]n + O₂ → CO₂ + H₂O

    • This process involves:

    • Losing electrons (Oxidation) and gaining electrons (Reduction).

    • Energy is released during the transfer of electrons from carbon to oxygen.

Cellular Respiration

  • Definition: The metabolic pathway in which glucose is fully oxidized to carbon dioxide.

  • Stages of Cellular Respiration:

    • Glycolysis

    • Pyruvate Oxidation

    • Citric Acid Cycle

    • Oxidative Phosphorylation

Glycolysis

  • Phases:

    • Energy Investment Phase:

    • ATP is used to phosphorylate glucose derivatives.

    • Energy Payoff Phase:

    • ATP is produced via substrate-level phosphorylation.

Citric Acid Cycle

  • Location: Mitochondrial Matrix.

  • Function:

    • Fully oxidizes Acetyl CoA to CO₂.

  • Yields per Acetyl CoA:

    • 1 ATP, 3 NADH, 1 FADH₂

  • Yields per Glucose:

    • 2 ATP, 6 NADH, 2 FADH₂

Oxidative Phosphorylation

  • Involves the electron transport chain and chemiosmosis to synthesize ATP.

  • Proton-Motive Force:

    • Established by the differential gradient of protons across the inner mitochondrial membrane.

    • Critical in ATP synthesis.

Mitochondrial Diagram

Photosynthesis

  • General Equation:

    • CO₂ + H₂O + Energy → [CH₂O]n + O₂

    • Fundamental processes: Oxidation (losing electrons) and Reduction (gaining electrons).

  • Energy storage occurs in the C-H bonds of carbohydrates.

Photosystem I & II

  • Photosystem II (PS II):

    • Involved in the initial stages of the light-dependent reactions, utilizing P680 as a primary acceptor.

  • Photosystem I (PS I):

    • Utilizes P700 and participates in photostasis activities to reduce NADP+.

  • Light Reaction Outputs:

    • NADPH, ATP, and molecular oxygen.

Global Biodiversity Timeline

  • Timeline illustrates major events in the evolution of life including mass extinctions and the emergence of major groups of organisms.

  • Shows the shifting diversity of life through speciation and extinction events across millions of years.

Protists: Overview

  • Division of the Protista kingdom into various subgroups based on evolutionary traits (e.g., Diplomonads, Euglenozoa, Alveolata).

Diplomonads & Parabasalids

  • Diplomonads:

    • Have modified mitochondria known as mitosomes.

  • Parabasalids:

    • Lacking functional mitochondria, but possess hydrogenosomes used for energy production under anaerobic conditions.

Giardia sp.

  • Description:

    • A parasite known to cause giardiasis.

  • Transmission:

    • Through drinking contaminated water; minimal number of organisms can cause illness.

  • Symptoms:

    • Severe diarrhea and intestinal cramps.

  • Treatment:

    • Pharmaceuticals available.

Euglenozoa

  • Characteristics:

  • Distinct presence of a flagellum made of tubulin.

  • Subdivided into:

    • Euglenids: Primarily photosynthetic; have characteristics like eyespots, chloroplasts, and contractile vacuoles.

    • Kinetoplastids: Defined by large mitochondria and kinetoplast; include species that are human pathogens like those causing African sleeping sickness.

Alveolata

  • Characteristics:

    • Identified by presence of alveoli.

    • Three main groups:

    • Dinoflagellates: Photosynthetic flagellates known for red tides and bioluminescence.

    • Apicomplexans: All are parasites requiring multiple hosts; example includes Plasmodium which causes malaria.

    • Ciliates: utilize cilia for movement and feeding.

Fungi

Basic Biology and Morphology:

  • Over 100,000 described species with an estimated 1.5 million existing.

  • Function as major decomposers, breaking down organic matter, with a unique method of absorptive nutrition involving hyphae.

Phylum Ascomycota & Basidiomycota

  • Ascomycota:

    • Distinguished by ascus as their spore-producing structure; includes various forms from yeasts to multicellular fungi.

  • Basidiomycota:

    • Known for mushroom-forming species that have basidia as spore-bearing structures, playing significant roles in ecosystem functioning as decomposers and mutualists with plants.

Conclusion

  • Understanding life processes such as cellular respiration and photosynthesis aids in grasping broader biological concepts and their implications in the ecosystem.

  • Understanding organisms such as protists and fungi allows for greater awareness of biodiversity and the ecological roles these organisms play.