AP Bio Unit 4

Redox reactions

Reduction/oxidizing agent completely or partially gains electrons, oxidation/reducing agent completely or partially loses electrons, electrons release energy as they fall down an energy gradient moving from a less to more electronegative atom, Ea prevents instant combustion of glucose, pyruvate oxidation = acetyl coA

NAD+

Oxidized form, accepts 2 electrons (along with 2 protons), coenzyme: RNA dinucleotide, involved in ATP and biomolecule synthesis, dehydrogenase enzymes remove 2 hydrogen atoms from substrates for its coenzyme, NAD+

NADH or NADH H+

Reduced form, carries/gives 2 electrons

FAD and FADH2

Oxidized form and reduced form, same as NAD+ and NADH but FAD and FADH2 involve lower energy electrons

Respiration formula

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

Cellular respiration

In nearly all life forms, breaks bonds between carbon in glucose, releasing electrons, allowing them to be picked up by NAD+ and FAD, can be aerobic or anaerobic (such as with Sulfate SO4 2-)

Glycolysis

At the cost of 2 ATP, 1 glucose is broken down into 2 G3P, 4 electrons are released in the next breakdown step, allowing 2 NAD+ to become 2 NADH, 4 ATP is produced through substrate-level phosphorylation in the final step that produces 2 pyruvates, which are large and charged molecules after carboxyl loses its H+ (acidic)

Mitochondrial transport

NAD+ break down 2 pyruvate into 2 acetyl and 2 CO2 (which diffuses out of the cell), the 4 electrons released from these bonds are picked up by 2 NAD+, forming 2 NADH, uses active transport but energy comes from the bond not ATP

Krebs or citric acid cycle

Catabolic, after mitochondrial transport, 2 acetyl bond with 1 coA each, then go through the krebs cycle, producing 4 CO2 (waste), 2 ATP (or 2 GTP in many animal tissue cells, either used as ATP or to make ATP), 6 NADH, and 2 FADH2 for the 2 acetyl CoA

Substrate level-phosphorylation

Synthesis of ATP by direct transfer of Pi from an intermediate to ADP, form of ATP synthesis in both glycolysis and krebs cycle

ETC (electrons)

NADH transfers its 2 electrons to proton pump 1, which pass through integral cytochrome Q to proton pump 2, and peripheral cytochrome C to proton pump 3, the electrons lose free energy as they move down the pumps, and are finally picked up by O2 at the end to produce H2O, FADH2 transfers its electrons at proton pump 2 through the iron atom in the prosthetic heme group of cytochrome Q

ETC (protons)

The free energy released by electron movement is used by the proton pumps to power diffusion of hydrogen ions into the intermembrane space, the protons then diffuse back into the matrix through a facilitated diffusion tube that contains the enzyme F1F0 ATP Synthase, which spins as H+ pass through and uses kinetic energy to synthesize ATP from ADP and Pi through oxidative phosphorylation (electrons from oxidized carriers) for about 2 protons that pass

Chemiosmosis

process in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as ATP synthesis, coupled with the redox reactions of ETC, 1 NADH pumps 10 H⁺ into the intermembrane space

ETC (carriers and total)

Electrons from NADH result in around 3 ATP, electrons from FADH2 result in around 2 ATP, which is why ATP total of respiration can be either 36 or 38, as FAD may pick up electrons in place of NAD+ during mitochondrial transport if they lose enough energy, or 30 or 32 ATP (if using 2.5 for each NADH and 1.5 for each FADH₂)

Brown fat cells

packed with mitochondria that have channel proteins that allow protons to flow back down their concentration gradient, allowing for release of heat through oxidation of fat without building up too much ATP

Fermentation

Oldest, primary ATP source for prokaryotes and unicellular eukaryotes, emergency ATP source for other lifeforms in absence of oxygen, ETC fails with no oxygen and no NAD+ is recycled for glycolysis, so 2 NADH produced in glycolysis reacts with 2 pyruvate to form either 2 ethanol + 2 CO2 or 2 lactic acid (lowers pH and denatures proteins), restoring 2 NAD+ and still gaining net 2 ATP, fermentation enzymes always active but if oxygen is present and binds to sensor on mitochondrial membrane, respiration takes priority

Catabolism (carbohydrates)

Animals obtain glucose and other monosaccharides by breaking down disaccharides

Catabolism (proteins)

Animals digest old proteins for amino acids to build new proteins and use enzymes to deaminate excess amino acids and convert them to glycolysis or kreb’s cycle intermediates, excreted ammonia NH3, urea, or waste

Catabolism (fats) Fats > carbs > protein for energy

Animals digest fat into glycerol and fatty acids, with glycerol converted into G3P (glycolysis intermediate) and fatty acids being broken down into two carbon fragments in beta oxidation and entering kreb’s cycle as acetyl coA, lots of energy stored in fatty acids, so their breakdown leads to produced NADH and FADH2

Anabolic pathways/biosynthesis

Essential amino acids must be directly obtained from diet, about 10 amino acids and some fat can be produced by diverting intermediates of glycolysis and kreb’s cycle to different pathways

Metabolic regulation

To save resources and prevent waste, cells uses feedback inhibition, respiration activity increases as ATP is needed, and drops as ATP builds up, phosphofructokinase is the enzyme of step 3 of glycolysis and is inhibited by ATP and activated by AMP, so glycolysis slows down with ATP production and speeds up as ATP breaks down into ADP and AMP, citrate, the first product of kreb’s cycle, also inhibits phosphofructokinase when it passes through the mitochondrial membranes into the cytosol as it builds up, if more ATP is needed or kreb’s cycle intermediates are siphoned for anabolic pathways, citrate concentration drops and glycolysis speeds up

Red muscle cells vs white muscle cells in mammals

In mammals, red muscle cells put glucose through respiration whenever possible, but white muscle cells always produce lactate from pyruvate after glycolysis, even when O₂ is present, lactate is oxidized by nearby red muscle cells or sent to live and kidney for glucose formation, technically not fermentation since oxygen is present

Obligate anaerobes vs facultative anaerobes

organisms that only carry out fermentation or anaerobic respiration, organisms that make enough ATP to survive from either fermentation or respiration

Photosynthesis equation

6CO₂ + 6H₂O + light energy (endergonic) → C₆H₁₂O₆ + 6O₂

Photosynthesis (C3)

Unlimited ATP, fixes carbon from CO2 into glucose and other biomolecules, composed of light reactions and dark reactions/Calvin cycle

Light

shorter wavelength = stronger energy of photon, visible light = 380 nm to 740 nm wavelength, absorption spectrum = graph plotting pigment's light absorption vs wavelength, spectrophotometer = machine that directs beams of light of different wavelengths through a solution of a certain pigment, measuring the fraction of light transmitted at each wavelength, violet-blue light around 540 nm and red light around 670 nm are optimal for photosynthesis, chlorophyll a and b absorb and reflect different light, making a appear blue green and b appear olive green, carotenoids: absorb violet and blue-green light, as well as absorbing and dissipating excessive light energy that would damage chlorophyll or interact with oxygen to form dangerous and reactive oxidative molecules

Photosystems

reaction-center complex surrounded by several light-harvesting complexes, reaction-center complex: organized association of proteins holding a special pair of chlorophyll a molecules and a primary electron acceptor (Pheophytin, modified C a), light-harvesting complex: various pigment molecules (chlorophyll b, carotenoids) bound to proteins, electrons drop right back to ground state from excited state if no primary electron donor present

Light reactions (electrons)

Occurs in thylakoid space/membrane, starts with light energy/photons hitting outer chlorophyll of PSII, which absorb that energy and pass it along to the core chlorophyll a P680, exciting its electrons and kicking them off, and those electrons are replaced by H2O’s electrons, released when split into O2 and protons, electrons move through integral cytochromes from PSII to a proton pump to PSI, where electrons bind to core chlorophyll a P700 and are energized by light again, then travel through ferredoxin to NADP+ reductase, where they, along with an H+, are picked up by NADP+ to form NADPH (Mg in chlorphyll b pigments, electrons weakly held so knocked off by light energy into PS2), (electrons back into magnesium ion in chlorphyll b of PSI)

Light reactions (protons)

The free energy released by electrons as they pass through the proton pump is used to power diffusion of protons from the stroma into the thylakoid space, protons then diffuse back into the stroma through cF1F0 ATP Synthase, which spins as H+ pass through and uses kinetic energy to synthesize ATP from ADP and Pi through oxidative phosphorylation (electrons from oxidized carriers), thylakoid space has a high H+ concentration, while the stroma’s is low

Cyclic photosynthesis

Variant of photosynthesis in which electrons go through a cycle between being re-energized at PSI and returning to the proton pump (involves fd and pc), does not produce any NADPH, so no biosynthesis/growth, but does produce ATP, occurs in lack of water

Mitochondria vs chloroplasts

ATP form in stroma

Calvin Cycle or the light independent/dark reactions

Anabolic, occurs in stroma, CO2 binds to ribulose bisphosphate or RuBP (sugar), catalyzed by RuBisCo, starting a cycle that produces G3P (1/2 glucose) halfway through, and requires -9 ATP and -6 NADPH (energy expensive), does not require sunlight and G3P used for biosynthesis, Carbon fixation: incorporation of carbon in CO₂ from the air into organic compounds, carbon in CO2 reduced into carbohydrates by NADPH electrons, ends with regeneration of RuBP

Plant leaf biology

Cuticle on outside as protection, epidermis, palisade layer of cells with lots of chloroplasts (heavy photosynthesis), vascular bundle (tube through which sugar leaves and H2O enters), sponge layer (exchange area), CO2 enters and H2O and O2 leave through stomata, stomata regulated by guard cells that open and close to control loss of resources (such as water), veins to transport water and sugar to roots

Photorespiration

stomata close in hot, dry conditions to preserve water, so less CO2 comes in, O2 reacts with RuBisCo instead of CO2, making RuBP trash (leads to new calvin cycle that uses lots of ATP and only produces 2 carbon sugar to CO2 by peroxisomes and mitochondria) and requiring ATP to recycle it for use, adaptations that prevent water loss also lead to photorespiration, since O2 cannot leave and CO2 cannot enter

C4 Photosynthesis

Meant to conserve H2O, practices spatial isolation, allows Calvin cycle with closed stomata, first product is 4 carbon compound, partially closes stomata when warm and dry, conserving water and letting CO₂ out, still makes sugar b/c requires less CO_2, begins in mesophyll cells (between surface and bundle-sheath cells) and completed in bundle-sheath cells, CO₂ incorporated into carbon compounds in mesophyll cells by PEP carboxylase, then calvin cycle occurs in bundle-sheath cells, ATP used in mesophyll cell cycle, produces CO₂ which goes to bundle-sheath cell for calvin cycle producing sugar to vascular tissue, more efficient with less resources (C3 BINDS WITH CO2, carrying down to calvin cycle area, then returning as C3 back to carry more)

CAM photosynthesis

Practices temporal isolation, at night stomata open, CO₂ stored as CAM (a C₄ compound), during the day stomata close, CAM converted back into CO₂, keeping [CO₂] > [O₂] to prevent photorespiration, close stomata during day and open during night to preserve water in heat but still take up CO₂ to incorporate into organic acids, organic acids stored in vacuoles, then in morning when light reactions are possible, CO₂ released from organic acids to incorporate into photosynthesis

Overview

green cells are autotrophic, others get organic molecules from those green cells through veins, usually provided as sucrose, photosynthesis produces more than needed, stores excess as starch in other parts of the plant, glycolysis in nearly every species, respiration controlled by allosteric enzymes (feedback inhibition), NAD+ = RNA, fungi = ethanol + CO2 fermentation, more steps = more chances for regulation and slower energy release, higher Rf/traveled further up paper = more soluble in solution, less in paper