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. Lab Vocabulary Trophic Levels Autotroph Heterotroph Primary consumer
Secondary consumer
Tertiary consumer
Producer
Decomposer
Most of the time, producers will be measured in how much sq. ft. they take up rather than number of species – however, for this assignment, go with number of organisms. However, you may want to record theirs as a multiple of 10 as there will be a LOT more than other organisms than there are producers.

5. 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?
The amount of organisms in trophic levels (energy levels) affect each other.
Therefore, changes in the energy available to an ecosystem fluctuates and so, too, does the organisms comprising the ecosystem.

6. 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?

7. 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?

8. 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

9. Offsetting Processes
In biological systems, within and between organisms, offsetting processes occur. The products of one reaction become the reactants of other reactions. However the input of energy must always be greater than the loss of energy over time (and energy is lost through heat and use).
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.

10. 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.

11. 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.

12. Order (Entropy)
Order is maintained through processes that increase entropy (and give off energy), combined with processes that decrease energy and “take in” energy into products.
More energy stored in a molecule means it is more ordered (the energy is nicely organized into a molecule) – this is a decrease in entropy.

13. Enthalpy – change in energy
When we burn wood, energy is released. When referring to simply the reactants and products, if the process releases energy, the change in energy is negative because we “lost” it.

14. 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.]

15. Gibb’s Free Energy
If energy is released (increase in free energy, increase in entropy), this is a negative or exergonic reaction (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.

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

17. Entropy
Enthalpy
Means disorder.
Means energy.

18. Spontaneity

19. Gibbs Free Energy Examples
Calculate ΔG using ΔG = ΔH - TΔS. Also, for each question, tell whether or not the reaction will be spontaneous (assume standard temp). a) CH3OH(l) + 1½ O2(g)  CO2(g) + 2 H2O(g) ΔH = kJ ΔS = J / K ΔG = *remember, we are going from J to kJ.* K = Kelvin
b) 2 NO2(g)  N2O4(g) ΔH = kJ ΔS = J / K
Standard Heats and Free Energies of Formation and Absolute Entropies of Elements and Inorganic Compounds (We don’t need this, but in chemistry, you would!)

20. Gibbs Free Energy Examples – Showin’ our work!
Calculate ΔG using ΔG = ΔH - TΔS. Also, for each question, tell whether or not the reaction will be spontaneous (assume standard temp – 25°C). a) CH3OH(l) + 1½ O2(g)  CO2(g) + 2 H2O(g) ΔH = kJ ΔS = J / K ΔG = *remember, we are going from J to kJ.* K = Kelvin

21. More Example!
b) 2 NO2(g)  N2O4(g) ΔH = kJ ΔS = J / K

22. More Advanced? Via Prairie South

23. Solution

24. Synthesis and Breakdown of ATP
Adenosine triphosphate (ATP) is a molecule that holds a lot of energy and is readily broken down in biological systems for energy. This release of energy would be an exergonic reaction as it breaks down into ADP.
ATP is synthesized using an input of free energy. This occurs in photosynthesis and cellular respiration.

25. 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?

26. 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?
FLIPGRID!

27. 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)? What is the evolutionary advantage and/or disadvantage of each? How does each regulate their body temperature?
Perform activities for:

28. 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)? What is the evolutionary advantage and/or disadvantage of each? How does each regulate their body temperature?
Perform activities for:
Growth.
Maintain organization.
Reproduce (when creating offspring, you need additional energy to grow these new organisms).

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

30. 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?).
How does our metabolic rate compare to that of mice and other small organisms?

31. Metabolic Rates
Smaller the organism – typically means a higher metabolic rate relative to their size – why might this be the case?
When organisms ingest more than they’re metabolic rate requires, they either grow or store energy (we store it as fat).
When they ingest less, energy is “found” through the breakdown of stored energy in fats, proteins and other parts of the body.

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

33. 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

34. 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.

35. Photosynthesis
Light-dependent reactions in eukaryotes capture free energy in light to make ATP and NADPH.
Chlorophylls absorb light, energizing electrons in PSII and PSI.
PSII and PSI 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.

36. Photosynthesis and Prokaryotes
Photosynthesis first evolved in prokaryotes (chlorophyll is in the cell membrane).
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.

37. Cellular Respiration
Series of enzyme-driven reactions that get energy from carbs.
Glycolysis rearranges bonds in glucose molecules, releasing free energy (exergonic) to form ATP from ADP and inorganic phosphate and a molecule called pyruvate, which is oxidized in the mitochondria in aerobic respiration (oxygen present).
Kreb’s (or The Citric Acid) Cycle carbon dioxide is released from the pyruvates variations to create more ATP and electrons are captured by coenzymes NADH, and FADH2 to be used in the electron transport chain.

38. Cellular Respiration – Electron Transport Chain
ETC captures free energy from electrons in a series of coupled reactions creating a concentration gradient (there’s one of these in photosynthesis and in the plasma membranes of prokaryotes too)!
NADH and FADH2 transport electrons into this chain where the electrons are accepted by molecules like O2. In the process we get a buildup of H+ protons which ATP synthase harnesses the energy of to make ATP from ADP.

39. Phosphorylation
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 (steal electrons from) nutrients, thereby releasing energy which is used to produce adenosine triphosphate (ATP). Phosphorylation specifically is the addition of a phosphate group.

40. 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) 

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

42. Carbon Cycle Carbon goes from environment (inorganic) to organisms.
Used to build carbs, lipids, proteins, and nucleic acids.
Required for energy storage and cell formation

43. Nitrogen Cycle
Nitrogen goes from environment (inorganic) to organisms (organic).
Used to build proteins and nucleic acids.
DNA, enzymes, structural components of body and cells (lots of things are made up of these).

44. Phosphorus Cycle
Phosphorus goes from environment (inorganic) to organisms (organic).
Used for certain lipids and nucleic acids.

45. 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?

46. 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

47. Surface Area to Volume Ratio 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.

48. 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.

49. 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.

50. 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)

51. Cell Membranes
Are selectively permeable! This is a result of it’s fluid mosaic model structure and phospholipid bilayer.
Separate the internal environment of the cell from the external environment.
What different components do you see in here? What are they?
By LadyofHats Mariana Ruiz - Own work. Image renamed from File:Cell membrane detailed diagram.svg, Public Domain,

52. Components of Cell Membranes
Phospholipids bilayer has both hydrophilic and hydrophobic properties.
Also has embedded proteins, cholesterols, glycoproteins and glycolipids! These can be hydro - philic (or –phobic) and have charged or non-polar side groups.
Some small uncharged polar molecules and small non-polar molecules may flow freely through the membrane (like N2).
Other molecules, like water, pass through embedded channel proteins (called aquaporin for water).

53. Different types of cell membranes/cell walls
What is this significance of each structure? How might each be applicable or relevant to the organism? “What does cellulose provide?”

54. Why are cell membranes important? Why are their differences significant?
Ideas?

55. Types of Transport
Chapter 5.2, 5.3, 5.4

56. Types of Transport Requires an input of free energy.
Active Transport
Passive Transport
Requires an input of free energy.
Net movement of molecules is from [low concentration] to [high concentration].
Does not require an input of free energy (simple diffusion is flows through membrane, facilitated diffusion flows via carrier proteins).
Net movement of molecules is from [high concentration] to [low concentration].
Facilitated diffusion and osmosis (movement of water) involves a type of passive transport of charged molecules via carrier proteins.
Important for incoming resources and outgoing wastes.
Facilitated Diffusion and Active Diffusion w/ Glucose
Different, specialized cells use different means of transport for same nutrient!

57. Comparing Solutions
Isotonic - a substance that has equal or balanced solute concentration when compared to another.
Hypotonic – a hypotonic substance has a low concentration when compared to another.
Hypertonic - a hypertonic substance has a high concentration when compared to another.
When a cell is in a hypertonic solution (high concentration), it will lose water to try to balance the concentration between itself and the solution it is in. When a cell is in a hypotonic solution (low concentration), it will take on water to have its concentration balanced with the surrounding solution.

58. Bulk Transport (large molecular active transport)
Endocytosis
Exocytosis
Cell takes in macromolecules or other particulate matter by forming new vesicles from the cell membrane.
Receptor-based (left) has a lot to do with our responses to drugs.
Vesicles inside the cell fuse with the cell membrane excreting macromolecules from the cell.
Involved in to release of neurotransmitters.

59. Comparison Chart!

60. Eukaryotes and Importance of Specialized Locations
Connecting cell membranes to surface area, when so many biological processes occur through cell membranes, having more surface area of particular cell membranes increase how much of a process can occur, as well as be more focused in what reactants/products are able to exit and enter certain membrane-bound organelle locations and their associated cell membranes (like a chloroplast/mitochondria).
Are there processes that may interfere with each other? Are the reactants of some also reactants for others? This too illustrates the necessity for compartmentalization in cells.
Prokaryotes lack these membrane-based organelles and do not have specialized regions which may diminish specialization/multitude of their functions.

61. Osmosis/Movement of Water Across Membranes Lab?
Data skills.
Inference skills based on data.
Does what you use achieve homeostasis based on the data we see?

62. Water Potential Calculations* *=confirm if needed.
Water potential integrates a variety of different potential drivers of water movement, which may operate in the same or different directions. Within complex biological systems, many potential factors may be operating simultaneously. For example, the addition of solutes lowers the potential (negative vector), while an increase in pressure increases the potential (positive vector). If flow is not restricted, water will move from an area of higher water potential to an area that is lower potential. A common example is water with a dissolved salt, such as sea water or the fluid in a living cell. These solutions have negative water potential, relative to the pure water reference. With no restriction on flow, water will move from the locus of greater potential (pure water) to the locus of lesser (the solution); flow proceeds until the difference in potential is equalized or balanced by another water potential factor, such as pressure or elevation. (1)