1. Big Idea 2
Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis.

2. Growth, reproduction, and maintenance, of the organization of living systems require free energy and matter.
Recommended reading: Chapter 6: Metabolism, OpenStax Biology

3. Constant inputs of energy
Life is incredibly complex and ordered (inter- and intra- organismally).
To function, constant inputs of energy are required.
Prolonged (dis)order = death.
Enthalpy relates to energy change (energy changes).
Living systems do not violate the second law of thermodynamics (entropy). What is this?
Increasing disorder is offset by biological processes that maintain or increase order. How might this work?
2nd Law = Entropy increases over time. Photosynthesis products are used as reactants in respiration.

4. Energy - Biochemistry What types of energy are there?
Where is energy stored?
How does energy get converted and subsequently stored?
Why might there be different amounts of energy in different types of macromolecules?

5. What is a biological process?
Explain some examples?
Biological processes “are the processes vital for a living organism to live. Biological processes are made up of many chemical reactions or other events that are involved in the persistence and transformation of life forms.”(1)
Examples (more on this later)
Calvin Cycle
Krebs Cycle
Light-Dependent Reactions
Glycolysis
Fermentation

6. Offsetting Processes
The products of one become the reactants of others. However the input of energy must always be greater than the loss of energy over time.
Cycle(s) of life, chemically, how does this look?
Series of negative feedback loops exist throughout nature. What are examples of these?
Certain things that consume energy are offset by processes that produce energy.

7. Feedback Loops
Negative feedback loops in nature typically are a good thing. The input is negated by the output.
Positive feedback loops in nature are typically a bad thing. The input produces and output which increases the input which produces more output Negative feedback loops maintain balance. Positive drives towards an extreme.

8. Free Energy
Thermodynamic quantity equivalent to the capacity of a system to do work.(1)
An exergonic reaction refers to a reaction where energy is released. Because the reactants lose energy (G decreases), Gibbs free energy (ΔG) is negative under constant temperature and pressure. (2) Some reactions require activation energy EA (energy to get the reaction going!)
Here is an endergonic reaction of ATP to give energy. Breaking down the ATP formed ADP and Pi is an exergonic reaction, where ΔG is less than 0.

9. Calculating Gibb’s Free Energy
ΔG = ΔH − TΔS ΔG = change in Gibbs free energy ΔS = change in entropy ΔH = change in enthalpy T = absolute temperature (in Kelvin = C° + 273)
From OpenStax, pg. 181: [The standard free energy change of a chemical reaction is expressed as an amount of energy per mole of the reaction product (either in kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = kcal) under standard pH, temperature, and pressure conditions. Standard pH, temperature, and pressure conditions are generally calculated at pH 7.0 in biological systems, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively. It is important to note that cellular conditions vary considerably from these standard conditions, and so standard calculated ΔG values for biological reactions will be different inside the cell.]

10. Gibb’s Free Energy
If energy is released (increase in free energy, increase in entropy), this is a negative or exergonic reactions (the products have less energy than the reactants).
If it is taken in (decrease in free energy, decrease in entropy), this is a positive or endergonic reaction.
If ΔH is negative (energy is released – decrease in enthalpy)
Look at each of the processes shown, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease? (a) a compost pile decomposing, (b) a chick hatching from
a fertilized egg, (c) sand art being destroyed, and (d) a ball rolling down a hill.

11. Graphing comparisons of Ender- and Exer-gonic Reactions
How do enzymes help when energy is required to make a product?

12. Gibbs Free Energy Examples
Calculate ΔG using ΔG = ΔH – TΔS (at standard temp, pressure). Also, for each question, tell whether or not the reaction will be spontaneous. a) CH3OH(l) + 1½ O2(g)  CO2(g) + 2 H2O(g) ΔH = kJ/mol ΔS = J / mol-K
b) 2 NO2(g)  N2O4(g) ΔH = kJ/mol ΔS = J / mol-K

13. In our bodies…
Certain things decrease energy required within us for reactions to occur.
What macromolecules are these things composed of?
How are these things made?

14. Select a Biological Process from our list before
These processes are “sequential” meaning they can be entered at any point. As a result, if I took a pill (not in Ibiza), that was full of NADH, how might that influence ethyl alcohol fermentation (would it increase/decrease the amount of alcohol and how?)
How might this apply to the supplements we take, what might they actually do when considering biological processes?

15. Why do organisms need energy?
What are examples of ectotherms (use of external thermal energy to help regulate and maintain body temperature)?
What are examples of endotherms (the use of thermal energy generated by metabolism to maintain homeostatic body temperatures)?
Perform activities for:
Growth.
Maintain organization.
Reproduce (when creating offspring, you need additional energy to grow these new organisms).

16. Varying Reproductive Strategies
When do many organisms reproduce (plants and animals)? Why would this make sense in terms of energy?

17. Metabolic Rates
Getting cats fixed affects their metabolic rates – resting metabolic rate.
Given your size – what is your resting metabolic rate? Link!
Mine is 1962 calories/day (8209kJ?).

18. In our labs
When you increased the amount of producers in a population, what should have happened to the total population of the community?
If you decreased decomposers, how might this impact the community?
Amount of organisms in trophic levels affect each other.
Therefore, changes in the energy available to an ecosystem fluctuates and so, too, does the organisms comprising the ecosystem.

19. In our labs - continued
Autotrophs (chemo- or photo-) convert free energy from inorganic components.
What types of different macromolecules do we (heterotrophs) get energy from?

20. Energy capturing needs Electron Acceptors
NADP+ in Photosynthesis
O2 in respiration.
Why?

21. Photosynthesis and Cellular Respiration flipped – you learn it, then come to class to discuss and talk it out
Chapter 8 of OpenStax Text
Chapter 7 of OpenStax Text

22. Reading Strategies Create and answer questions about the content.
Provide summary of each section/highlight or make keys points or ideas you thought were important.
Complete end of chapter summaries found in the textbook.
This reminds me of (connect to previous things you know).
Try to teach it to someone else.
Make predictions about the start of chapter objectives.
Create a drawing or visual to better “see” the content.

23. Make Questions about P and CR using the curriculum
What are

24. Photosynthesis
Light-dependent reactions in eukaryotes capture free energy in light to make ATP and NADPH.
Chlorophylls absorb light, energizing electrons in PII and PI.
PII and PI are embedded in the membranes of the thylakoid in chloroplasts and are connected by the transfer of these electrons through a series of other molecules in the electron transport chain (ETC).
As these electrons are transferred via reactions in the ETC, water is split to replenish lost electrons and contributes to a buildup of H+ (protons) causing an electrochemical gradient.
This proton gradient is harnessed by an enzyme to create ATP from ADP and an inorganic phosphate.
The energy captured and stored into ATP and NADPH powers the production of carbohydrates from carbon dioxide in the Calvin cycle, which occurs in the stroma of the chloroplast.

25. Photosynthesis and Prokaryotes
Photosynthesis first evolved in prokaryotes (chlorophyll is in the cytoplasm).
Evidence supports that this is what oxygenated our atmosphere.
Prokaryotic photosynthetic pathways are foundation of photosynthesis but instead occurs in their plasma membranes than organelle-based pathways (much like respiration in the mitochondria).
Think of endosymbiotic theory. Rather than getting water and CO2 from inside the cell, it got it from the surrounding environment.

26. Cellular Respiration

27. Free energy ultimately becomes available for metabolism by converting ATP  ADP, which is a big part of many steps in metabolic pathways (occurring by that H+ buildup and chemiosmosis).
What are structural features and mechanisms allow organisms/cells to capture, store, and use free energy?
Construct a graph of free energy in a system starting from light  photosynthesis  respiration.
Oxidative phosphorylation – is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing energy which is used to produce adenosine triphosphate (ATP). Phosphorylation specifically is the addition of a phosphate group.

28. Biological Energy Processes
Summarize the process - How is the energy obtained? What is the energy specifically obtained from/converted? - What molecules are electron acceptors in the process? - How is an electrochemical gradient involved? Autotrophs (inorganic --> organic) --> Chemosynthesis --> Photosynthesis Heterotrophs (organic --> organic) --> Metabolism of carbs, lipids, and proteins for energy --> Fermentation (lactic acid or ethyl alcohol) 

29. Organic Molecules
Chapter 2 and 3 (Atoms, Water and Organic Molecules) of OpenStax Text

30. Carbon Cycle

31. Nitrogen Cycle

32. Phosphorus Cycle

33. Water
Water is polar! What does this mean? Why is it important? Why is it polar?
Is hydrogen-bonding strong or weak?
Reminder: What is diffusion (active/passive transport), what are cell membranes composed of, and why is this relevant to nutrient uptake?

34. Water – why are each of these properties so significant to life?
Cohesion
Adhesion
High specific heat capacity
Universal solvent supports reactions
Heat of vaporization
Heat of fusion
Water’s thermal conductivity

35. Surface to Area Volume in Uptake
As cells get bigger, their surface area to volume ratio decreases.
If interested in maximizing the ability to take in nutrients and dispose of waste, what is the most practical “design” when organizing cells?
Is having larger cells smart then? Why might some of our human body cells be bigger than others when considering its “needs” or function.

36. Structures that utilize this concept.
Root hairs (tinier roots can lead to greater water uptake).
Cells of alveoli (in our lungs, maximizes diffusion of CO2 and O2
Villi (part of our digestive tract)
Microvilli (cellular protrusions)
Larger cell membrane surface areas provide more opportunities for nutrient exchange.

37. Applying this concept mathematically Cylinder SA = 2πrh+2πr2
Cell Type – Surface Area and Volume
Surface area to volume ratio
Which of the following cells likely is able to have the greatest uptake of nutrients and loss of waste.
A spherical red blood cell that has a diameter of 20µm.
A cylindrical root hair that has a height of 800µm and a diameter of 30µm
A cube-shaped plant stem cell that is 40µm long, wide, and tall.
A rectangular animal bone cell that is 50µm long, 30µm wide, and 40µm tall.

38. Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments.
Recommended Readings: Chapter 5 – Structure and Function of Plasma Membranes (OpenStax)