AP Biology/Cellular Energetics

Introduces how cells interact with their environment and how fundamental biological processes work at the cellular level.

Objectives and Skills
Topics may include:
 * The structure and function of enzymes
 * The role of energy in living systems
 * The processes of photosynthesis
 * The processes of cellular respiration
 * Molecular diversity and cellular response to environmental changes

Study Notes
Study of energy transformations that take place in a collection of matter
 * Metabolism - Total of all chemical reactions in a cell; the emergent property of life that arises from interactions between molecules within a cell.
 * Chemical Energy - Stored energy in cells.
 * Energy - Capacity to change
 * Enzyme - [reusable] Needed for every chemical reaction; finds substrate by cladding with the substrates; an organism's metabolism transforms matter and energy, subject to the laws of TD.
 * Induced Fit - Enzyme alters its shape to bind together to its substrate.
 * Metabolic pathway - Begins with a specific molecule and ends with a product.
 * Activation Energy - Minimum amount of energy needed to kickstart a reaction (enzyme lowers the activation energy).
 * Catabolic - Breaking something down (cellular respiration).
 * Anabolic - Putting something together (synthesis of a protein).
 * Energy Coupling - Energy from a catabolic reaction to an anabolic reaction.
 * Laws of Thermodynamics
 * 1st Law: Energy converts from one form to another, not destroyed.
 * 2nd Law: Energy transformation increases the entropy of the universe (waste product is heat, the most disordered type of energy that exists).


 * Spontaneous Process - If a given process, by itself, leads to an increase in entropy, that process can take place without requiring an input of energy. Nonspontaeous processes occur if energy is supplied.
 * Rate of Reaction - R=change in concentration/change in time
 * Reverse/Forward Reaction - Increase the reactants --> increasing the forward reaction; increase the products --> increasing the reverse reaction.
 * An addition of catalase would increase the reaction rate of both reactions.

Enzyme Regulation

 * Activators - Molecules that increase the activity of an enzyme.
 * Inhibitors - Molecules that decrease the activity of an enzyme.
 * Reversable inhibitors
 * Competitive Inhibitors - Inhibitor "competes" with the substrate for the enzyme. Blocks binding of the substrate.
 * Noncompetitive Inhibitors - Inhibitor binds to another site on the enzyme, denaturing the protein by altering the shape.

Increasing the substrate concentration can outdo a competitive inhibitor (to the point that all the enzyme's active sites are occupied with substrates). Noncompetitive inhibitors can outdo substrates, even if the substrate concentration is high. Form of regulation where the regulatory molecule, an activator or inhibitor, binds to an enzyme other than the active site. The place where this binding takes place is known as the allosteric site.
 * Allosteric regulation

Allosteric enzymes have multiple active sites on different protein subunits. They display cooperativity, where the substrate can be an allosteric activator (the substrate binds to one allosteric site causing the activity of another allosteric site to go up).

When allosteric inhibitors bind to an allosteric site on an enzyme, they cause all of the active sites on the protein subunits to change (shape alters) so they work less well.

When allosteric activators bind to an enzyme, they increase the function of the active site.
 * Cofactor - Non-protein molecules that aid enzymes. Examples of these cofactors are inorganic ions, like iron.
 * Coenzymes - Subset of cofactors-these are organic (carbon) based, like vitamins. Some vitamins are initiated before coenzymes in a metabolic pathway while other vitamins act as coenzymes.

Enzymes are compartmentalized, meaning they're stored in a certain part of a cell where they do their job. This ensures that they can slide with their substrates and not do damage to the cell. Feedback inhibition, the end product of a metabolic pathway, occurs by acting on the key enzyme regulating the metabolic pathway so that the process stops and the enzyme won't overproduce that product.

Reactions

 * Exergonic - A chemical reaction where heat has been released. It is spontaneous/energetically favorable. There is more energy in the bonds of the reactants than in the bonds of the products.
 * Endergonic - A chemical reaction where heat has been absorbed. It is nonspontaneous. There is more energy in the bonds of the products than in the bonds of the reactants.

Cellular Respiration

 * Cellular Respiration: Glucose is converted into smaller units of ATP [ATP - Energy molecule of the cell ($10 [glucose] --> 10 $1 bill [ATP])]

Sun →Radiant Energy  Photosynthesis  →Glucose (stored chemical energy)  Respiration  →ATP (usable chemical energy)  Cell Activities


 * How is ATP used?
 * Transport work: ATP phosphorylates transport proteins.
 * Mechanical work: ATP phosphorylates motor proteins.
 * Chemical work: ATP phosphorylates key reactants.


 * Oxidation = Reduction reactions transfer energy within living organisms [release of energy].
 * Reduction = Stores energy in atom/molecule.

Whenever one substance is oxidized, another substance is reduced.

NAD+ can be used to carry electrons. The final acceptor for CR is O2 [acts a magnet for electrons].

Oil Rig

 * Oxidation = Lose energy
 * Reduced = Gains energy

Stages

 * Glycolysis - Breaks down glucose and converts to pyruvate. Applies to all processes. Net production: 2 ATPs. NAD+ connects to NADH. When it picks up electrons and takes them to ETC. It takes place in the cytosol.

Without Oxygen

 * Pyruvate enters a eukaryotic cell with oxygen to convert to acetyl CoA. Then iff it has no oxygen, then fermentation takes place. In the process of fermentation, NAD+ [from NADH] and CO2 is produced and the process goes back to Glycolysis. Vitamin A is involved, which facilitates the reaction that occurs - before the Kreb's Cycle. The Kreb Cycle begins from the oxidation of acetyl-CoA. Occurs frequently in yeast (alcoholic fermentation), lactic fermentation takes place. Amino acids and fats also undergo cellular processes.

With Oxygen

 * Kreb Cycle/Citric Acid Cycle - Acetyl CoA goes through a cycle of reactions, where ultimately carbon dioxide is produced and net production of 2 ATP occurs. NADH and FADH2, carrying electrons to the ETC, are produced. ATP is produced in both reactions by ADP + Pi --> ATP.
 * ETC and Oxidation Phosphorylation - The NADH from glycolysis and Krebs and the FADH2 come to the ETC. Here, the NADH is oxidized into NAD+. The 2e- and 2H+ from the NADH is combined with half of an oxygen molecule (the final acceptor) to create H2O (water). Before the electrons combine with the O2, it goes through a bunch of electron acceptors and releases energy along the way. The energy is used to pump H+ across the membrane (against the concentration gradient). The H+ goes through ATP Synthase groups ADPs with phosphate groups with the energy of H+ to form ATP. Meets with half of the oxygen and water is produced.

34 ATP is formed through oxidation phosphorylation, the oxidation of NADH/FADH2. Water is also produced as a byproduct.

Review: https://www.google.com/search?q=cellular+respiration+diagram&safe=strict&sxsrf=ALeKk03yIp5RtT79GR_vpV9k6ho9h1C8UQ:1589071206579&tbm=isch&source=iu&ictx=1&fir=WTkIbu14DYuwpM%253A%252CPsKefdi7ImJbZM%252C_&vet=1&usg=AI4_-kQkLVmiSXCRQD4OsTcvfZtSeg_pXg&sa=X&ved=2ahUKEwi1xqnGh6jpAhXEl3IEHRCuCgMQ9QEwAHoECAQQMA#imgrc=WTkIbu14DYuwpM

Photosynthesis

 * Heterotrophs (consumer) get energy from other organisms (cellular respiration).
 * Autotrophs (producers) get energy from the sun (photosynthesis).
 * Consists of
 * 1) Light-Dependent: Light Reactions [thylakoid] (produce: ATP, NADPH and O2 - used for below)
 * 2) Light-Independent: Dark Reactions [calvin cycle; stroma] (CO2, hydrogen from NADPH and ATP --> glucose)

Photosynthesis takes place in the chloroplast except for bacteria. It takes only 1% of the sun's energy. Most life is powered by the sun. A stack of thylakoids is a granum.

Plants need M, C, H, O, N, P and S (elements). Sugar is made and moved to a certain part of the plant: sink. Photosynthesis performs work only with certain absorbed wavelengths of light.

SEE Photosynthesis [see the photo for more info on the 3 stages in the Calvin Cycle]

Evolution
Adaptation to thrive in dry habitats by using special compounds to capture CO2. It allows them to extract more air and prevent water loss in dry climates. Rubisco is not very good at getting CO2. When CO2 levels are low, rubisco mistakenly grabs oxygen. Photorespiration ends up burning up sugar instead of creating it, causing problems for the plants, who have to keep their stomata shut in order to prevent water loss. To counter this problem, the C4 and CAM plants do...

C4

 * Attach CO2 to PEP, phosphoenolpyruvate, to form OAA, oxaloacetate, with the help of PEP carboxylase. This occurs in the mesophyll cells.
 * OAA is pumped to the bundle sheath cells (surrounds the leaf vein). CO2 is released to Rubisco for use.
 * CO2 being concentrated in the bundle sheath cells promote efficiency and less of photorespiration.

CAM

 * Instead of fixing carbon during the day and pumping OAA to the bundle sheath cells, CAM plants fix carbon at night and store the OAA in large vacuoles.
 * Stomata opens at night = Avoid water loss.
 * Use CO2 from stomata to the Calvin Cycle during the day.