unit 3: cellular energetics

topic 1: thermodynamics

1st law of thermodynamics - energy cannot be created or destroyed

2nd law of thermodynamics - entropy of an isolated system can never decrease; the universe moves toward more disorder

entropy (S) - measure of disorder

metabolism - chemical processes within an organism that sustain life

anabolism - builds up; endergonic; non-spontaneous; ∆G > 0

catabolism - breaks down; exergonic reaction; spontaneous; ∆G < 0

gibs free energy (∆G) - measure of spontaneity of a reaction

spontaneous reaction - happens without any outside energy

∆G (equation) - ∆H-T∆S

H - enthalpy; heat of a reaction

T - temperature

endothermic reaction - absorbs heat; +∆H

exothermic reaction - releases heat; -∆H

∆G ATP Hydrolysis - -7.3kcal/mol

ATP coupled reaction - combining a non-spontaneous reaction with ATP hydrolysis can make the reaction spontaneous

rate of a reaction (factors) - higher reactant concentration; higher surface-area of reactants; higher temperatures; free catalysts

catalysts - increases the rate of reaction by lowering the activation energy (E_a); not changes / used up by reaction

common exergonic reactions - hydrolysis of ATP; cellular respiration

common endergonic reactions - phosphorylation of ADP; photosynthesis

topic 2: enzymes

enzyme - biological catalyst; made of protein; -ase

substrate - reactants in a reaction

active site - size where substrate attaches to enzyme

lock and key model - outdated; substrate fits perfectly into the active side

induced fit model - active site undergoes conformational change as substrate binds

coenzyme - non-protein organic compounds required for enzyme activity; part of active site; ex: vitamins

cofactor - non-protein inorganic compounds required for enzyme activity; ex: minerals

apoenzyme - protein part of enzyme

holoenzyme - whole enzyme; non-protein and protein

enzyme temperature - operate at optimum ____; can differ within species

enzyme pH - operate at optimum _____; can differ within organism

denatured proteins - disrupted secondary/tertiary/quaternary structure; too far out of optimal condition; often irreversible

peptide bonds - not broken in denatured proteins

protein folding - not repeatable: order out of ribosome, golgi apparatus modifications, + protein chaperones

competitive inhibitor - bind to active site; stop substrate directly/slowly

noncompetitive inhibitor - bind to allosteric site; stop substrate indirectly/quickly

allosteric activator - bind to allosteric site; activates enzyme

allosteric inhibitor - bind to allosteric site; alters enzyme

topic 3: photosynthesis

photosynthesis - produce sugars from light energy; used by autotrophs

chemosynthesis - produce sugars from chemical energy; used by autotrophs

cellular respiration - produce ATP from sugar and oxygen; used by autotrophs and heterotrophs

fermentation - produce ATP from sugar without oxygen; used by autotrophs and heterotrophs; alcoholic or lactic acid

cyanobacteria - possible ancestor of chloroplast

chloroplast - outer membrane → intermembrane space → intermembrane → stroma → granum → thylakoid membrane → thylakoid → lumen

granum - stack of thylakoids

lumen - inside of thylakoid

chlorophyll - releases high energy electron when hit by light; needs to be reset

light reactions (location) - occurs in thylakoid membrane

calvin cycle (location) - occurs in stroma

light reactions (components) - electron transport chain; atp synthase

light reactions (reactants) - H₂O; NADP⁺; ADP

calvin cycle (reactants) - CO₂; NADPH; ATP

light reactions (products) - O₂; NADPH; ATP

calvin cycle (products) - C₆H₁₂O₆ (glucose); NADP⁺; ADP

electron transport chain (photosynthesis) - PSII → cytochrome b → PSI; H₂O → O₂ & H⁺ + e-; NADP⁺ → NADPH

photosystem ii - reset by low energy e^- from H₂O; energizes e^- with light; passes e^- to cytochrome b

cytochrome b - hydrogen pump; energy from PSII e^-; passes low energy e^- to PSI

photosystem i - reset by e^- from cytochrome/PSII; energizes e^- with light; turns NADP⁺ + e^- + H⁺ → NADPH

atp synthase - synthesizes ATP; H⁺ concentration gradient spins; ADP → ATP

calvin cycle (components) - carbon fixation; reduction; regeneration

carbon fixation - rubisco brings in CO₂

reduction - ATP and NADPH used to create 6 G3P

regeneration - 5 out of 6 G3P recycled in cycle

glycerol 3 phosphate (G3P) - 2 used to make 1 glucose

photorespiration - calvin cycle rubisco takes in O₂; requires energy to fix

photorespiration (cause) - worsened by high O₂ concentrations (light reactions) + low CO₂ concentrations (calvin cycle)

stomata - structures under leaf; gate for gas exchange; usually closed at night to prevent water loss

c3 plants (what) - standard photosynthesis; most efficient

c4 plant (what) - separation mitigates photorespiration; more energy intensive

cam plant (what) - timing + high CO₂ mitigates photorespiration; more energy intensive

c4 plant (how) - light reaction in mesophyll cell (more O₂); calvin in bundle-sheath cell (less O₂)

cam plant (how) - stomata gathers CO₂ at night; CO₂ stored as malic acid in vacuole; malic acid converted to CO₂ at daylight

c3 plant (environment) - excels in wet environment; stomata rarely closes during day

c4 plant (environment) - excels in dry environment; stomata often closes during day

cam plant (environment) - excels in very dry environment; stomata closed during day

topic 4: cellular respiration

ventilation - physical movement of gasses into and out of the lungs

respiration - movement of gasses across a membrane

cellular respiration - creating ATP from C₆H₁₂O₆ (glucose) and oxygen

aerobic respiration - uses oxygen; ex: cellular respiration

anaerobic respiration - does not use oxygen; ex: fermentation

mitochondria - outer membrane → intermembrane space (acidic) → inner membrane → cristae → matrix

glycolysis (definition) - starting point of anaerobic and aerobic respiration; anaerobic

glycolysis (reactants) - C₆H₁₂O₆ (glucose); NAD⁺

glycolysis (products) - 2 pyruvate; NADH; 2 ATP

glycolysis (location) - occurs within cytoplasm

krebs cycle (definition) - oxidization of pyruvate; aerobic

krebs cycle (reactants) - 1 pyruvate

krebs cycle (products) - 2 CO₂; 3 NADH; 1 FADH₂; 1 ATP; H⁺

pyruvate dehydrogenation - pyruvate + coenzyme a → acetyl-co a + CO₂ + NADH + H⁺

krebs cycle (location) - occurs within matrix

oxidative phosphorylation (definition) - cellular respiration; electron transport chain + ATP synthase; powered by krebs cycle

oxidative phosphorylation (reactants) - NADH; FADH₂

oxidative phosphorylation (products) - 32-34 ATP; H₂O; NAD⁺; FAD; H⁺

oxidative phosphorylation (location) - occurs within matrix

complex i - reset by e^- from NADH; pump H⁺ into intermembrane space; passes on e^- to complex iii

complex ii - reset by e^- from FADH₂; passes on e^- to complex iii

complex iii - reset by e^- from complex i and complex ii; pump H+ into intermembrane space; passes on e^- to complex iv

complex iv - reset by e_^- from complex iii; pump H⁺ into intermembrane space; passes on e_^- to O₂ (creating H₂O); 2H⁺ + ½O₂ + 2e_^- → H₂O

electron transport chain (cellular respiration) - complex i; NADH → complex ii; FADH₂ → complex iii → complex iv; O₂ → H₂O

carbs (to ATP) - sugar → glucose → glycolysis

fats (to ATP) - fatty acids → acetyl-co a; glycerol → glycolysis

proteins (to ATP) - amino acids (remove NH₃) → pyruvate dehydrogenation or krebs cycle

anaerobic respiration - ATP from only glycolysis; NAD⁺ from lactic acid fermentation or alcoholic fermentation

H₂O - created by complex iv; used by photosystem ii

NADPH / NADP+ - energized by photosystem i; used by calvin cycle’s reduction

ATP / ADP - energized by atp synthase, glycolysis, krebs cycle, oxidative phosphorylation; used by calvin cycle’s reduction

CO₂ - created by pyruvate dehydrogenation; used by carbon fixation

O₂ - created by photosystem ii; used by complex iv

C₆H₁₂O₆ (glucose) - created by calvin cycle; used by glycolysis

NADH / NAD⁺ - energized by glycolysis, pyruvate dehydrogenation; used by complex i

FAD / FADH₂ - energized by krebs cycle; used by complex ii