ap bio unit 3

3.1 Enzyme Structure
Enzymes: biological catalysts that speed up biochemical reactions (lowers activation energy)
- most are proteins with region called active site
- tertiary shape must be maintained for functionality
- reusable as they are not chemically changed by the reaction
- maintain a specific enzyme []
- facilitates synthesis or digestions reactions
Substrates: molecule that can interact with enzyme
- name often indicates substrate involved and often ends with -ase
- E.g. sucrase is an enzyme that digests sucrose
Active Sites: location on enzyme that interacts with substrates
- unique size + shape that may have chemical charges
- physical and chemical properties of substrate must be compatible
- slight chances in active site → aligns with substrate

3.2 Enzyme Catalysis
Enzymes: biological catalysts, typically proteins to speed up biochemical reactions
- structure is very specific → only facilitates one type of reaction
- E.g. synthesis or digestion
Synthesis lowers activation energy
- all biological reactions require activation energy || typically reactions result in net release of energy, thus need less activation required than net absorption
Experiments:
- control group and experimental test group
- control group used as a standard for comparison (also known as constants)
E.g. Negative control group → not exposed to experimental treatment → no response expected
Positive control group → exposed to treatment with known effect

3.3 Environmental Impacts on Enzyme Function
- change in molecular structure (tertiary) of an enzyme → results in loss of enzyme function
- changes in the shape → denaturation → can be caused by environmental temperatures, pH → typically irreversible, some cases is reversible
E.g. optimum temperature (enzyme-mediated reactions occur the fastest
environmental increase in temperature → increased reaction rate → increased speed of molecular movement (think slope and rate)
- environmental decrease in temperature does not denature enzyme if structure is the same
E.g. pH measures [] of hydrogen ions in solution (log scale, basically a little pimple bump)
- small changes in pH value equites to large shift in h+ []
- optimum pH is the range where e-m r occurs the fastest
- enzyme denaturation can occur as a result of increases and decreases outside optimum → can cause denaturation as pH changes can disrupt h-bond that maintains enzyme structure
E.g. initial increase in substrate concentration increases reaction rate → more substrates = higher chance to collide with enzyme
- rate of reaction will plateau as substrate saturation will occur, more product = lower chance of enzyme-substrate collision (slower reaction)
- changes in enzyme [] can change impact reaction rate
→ less enzyme = slower reaction rate
→ more enzyme = faster reaction rate
Competitive Inhibitors: molecules that reversibly or irreversibly bind to active sites of the enzyme
→ competes with normal substrate for enzyme’s active site
→ inhibitor [] exceeds substrate concentration, then reactions are slowed
Noncompetitive Inhibitors: molecules that do not bind to the active site but still change enzyme activity (not direct)
→ binds to allosteric site (the side piece on the enzyme)
→ causes conformational shape change, and prevents enzyme function as active site is no longer available
→ increasing substrate cannot prevent effects of noncompetitive inhibitor binding

3.4 Cellular Energy
- sunlight is main energy input for living systems
- Autotrophs capture energy from physical sources (e.g. sunlight or chemical)
→ during every energy transformation (light to chemical), light is released
- life requires a highly ordered system that does not violate the second law of thermodynamics
→ every energy transfer increases the disorder of the universe
→ living cells are not at equilibrium → constant flow of materials in and out
→ cells manage energy resources by energy coupling → energy-releasing processes drive energy-storing processes
- the product of one reaction as serve as a reactant in a subsequent reaction
→ allows for a more controlled and efficient transfer of energy

3.5 Photosynthesis
photosynthesis: biological process that captures energy from the sun and produces sugars
→ prokaryotic photosynthesis by organism (such as cyanobacteria) → produced oxygen in atmosphere
→ photosynthetic pathways are the foundation of eukaryotic photosynthesis
light-dependent reactions: captures light energy using light-absorbing molecules called pigments
→ transforms light into chemical, chemical temporarily stored in chemical bonds of carrier molecules called NADPH
→ help facilitate ATP synthesis
→ ATP and NADPH transfers stored chemical energy to power the production of organic molecules in Calvin cycle
→ oxygen produced as a result of hydrolysis
chlorophylls: absorb energy from the light → capture light and convert it to high-energy electrons
→ electrons become energized, thus will establish a proton (+) gradient and reduce NADP+ to NADPH
photosystem I and II: embedded within the internal membranes of chloroplasts
→ light-capturing unit in a chloroplast’s thylakoid membrane
→ hydrolysis of water is necessary as hydrogen molecules from water are released into the thylakoid space → creates an electrochemical/proton gradient
electrochemical/proton gradient is the difference in concentration of protons (h+) across a membrane
→ photosynthesis uses a form of passive transport to ADP → ATP
ATP synthase: enzyme that creates ATP when protons pass through enzyme (due to proton gradient)
→ electrons follow electron transport chain (ETC)
→ PSII and PSI are related as they pass high-energy electrons to ETC
Calvin Cycle: uses ATP, NADPH, and Co2 and produces carbohydrates
→ makes organic products that plants need using the products from the light reaction of photosynthesis
→ plants + other organisms get carbon dioxide from the environment (not lithosphere)

3.6 Cellular Respiration
Fermentation and cellular respiration are processes that allows organisms to use energy stored in biological macromolecules
→ characteristics in all forms of life
→ release chemical energy from organic molecules (glucose)
→ oxygen is not required in fermentation, but required in cellular respiration
→ fermentation and anaerobic respiration are NOT the same process (fermentation produces lactic acid or ethanol, anaerobic still has pyruvate)
fermentation: allows glycolysis to proceed in absence of oxygen
cellular respiration (in eukaryotes): series of coordinated enzyme-catalyzed reactions that capture energy from biological macromolecules
→ includes glycolysis (glucose to pyruvic acid), Krebs cycle, electron transport
→ release of chemical energy through break down of glucose and creates an energy-storing molecule called ATP (used by all cells)
→ involves multiple metabolic pathways:
→ glycolysis → occurs in cytoplasm
→ pyruvate oxidation → occurs in mitochondria
→ Krebs cycle (citric acid cycle) → occurs in mitochondria
→ electron transport → occurs in mitochondria
electron transport chain: transfers energy from electrons in a series of coupled reactions
→ used during cellular respiration (conserved process) → located in inner mitochondrial membrane (needs membrane to create gradient)
→ more control + efficient transfer of energy
→ uses electron energy to establish proton gradient across membranes
→ electrons delivered by electron carriers → NADH, FADH2 (donated)
→ active transport of H+ occurs during ETC reaction
→ ATP synthase uses the electrochemical/proton gradient to synthesize ATP
→ gradient maintained as a result of membrane impermeability to charged molecules
chemiosmosis: flow of chemiosmosis through ATP synthase drives ATP synthesis
→ NADH and FADH2 lose high energy electrons to ETC (oxidation LEO GER)
→ ATP synthase adds an inorganic phosphate (Pi) to ADP → resulting in ATP molecule is called phosphorylation
In cellular respiration, decoupling oxidative phosphorylation from ETC generates heat
→ energy is stored in proton gradient → released as heat after taking apart (decoupling)
→ used in humans to regulate body temperature
→ refers to proton gradient not being used by ATP synthase to produce ATP
glycolysis: releases energy stored in glucose
→ results in pyruvate, NADH, ATP
pyruvate: transported from cytosol to the mitochondrion, actively transported
→ oxidized (lose electron), and a product of pyruvate oxidation enters the Krebs Cycle
Krebs cycle: carbon dioxide is released from organic intermediates:
→ carbon dioxide being released from intermediate reactions
→ high energy electrons transferred to NADH and FADH2
ADP is phosphorylated to form ATP
- electrons removed during glycolysis and Krebs are transferred to ETC
→ NADH created in glycolysis, ADH and FADH2 created Krebs cycle, and donate electrons to ETC (establish h+ gradient)
ATP hydrolysis: ATP → ADP when energy is released when chemical bonds are broken
→ bonds between 2nd and 3rd phosphate is broken
→ can power other metabolic processes

3.7 Fitness
- variation in cells can be evident on a cellular and molecular level
→ differences in molecular structure, types, proteins, carbs, lipids, number of molecules
individual fitness: individual organism’s being able to survive AND reproduce
→ more variation = higher chance species does well in wide variety of habitats
E.g. chlorophyll molecules vary within plant cells → different types of chlorophyll capture light energy at different wavelengths
E.g. cell membrane of animal cells have cholesterol while plant cells do not.
→ cholesterol regulates membrane fluidity → maintains fluidity at low temps, and stabilizes at high → need for homeostasis
→ decrease water penetration
→ animal cells do not have cell walls like plants to do counter lysis
→ increasing cholesterol can restrict diffusion of water through bilayer
E.g. Hemoglobin is a molecule that carriers oxygen in blood → two types found in humans
→ Hemoglobin F (fetal hemoglobin) allows efficient transfer of oxygen from blood of the mother to the fetus
→ Hemoglobin A (adult hemoglobin) binds oxygen brought in by lungs and aids in oxygen delivery to body cells