AP Bio Unit 3 - Barron’s 2020

First law of thermodynamics

aka law of conservation of energy; energy cannot be created or destroyed, only transformed from one form to another

Second law of thermodynamics

during energy conversion, entropy (disorder) increases

Exergonic reaction

aka exothermic; reaction in which energy is released; G < 0; SPONTANEOUS

Endergonic reaction

aka endothermic; reaction in which energy is absorbed; G > 0

Energy coupling

in biological systems, use of exergonic reactions to power endergonic reactions (ex. ATP (exergonic) powers Na-K pump (endergonic))

Metabolism

sum of all chemical reactions that take place in a cell

Catabolism

reactions that BREAK DOWN molecules

Anabolism

reactions that BUILD UP molecules

Metabolic pathways

series of metabolic reactions controlled by enzymes that let cells carry out chemical activities with EFFICIENCY

Enzyme

globular protein with tertiary structure; LOWERS ACTIVATION ENERGY OF REACTION; orients substrate molecules into positions that favor reactions to occur; catalytic protein; DOES NOT provide energy; DOES NOT enable reaction that wouldn’t have happened on its own; catalyze in BOTH directions (reversible); often need assistance from cofactors or coenzymes

Enzyme structure

globular protein with tertiary structure

Energy of activation

amount of energy needed to begin a reaction

Transition state

Reactive (unstable) version of substrate after sufficient energy absorbed to initiate reaction

Induced-fit model

as substrate enters active site of enzyme, it induces it to alter its shape slightly so substrate fits better (lock and key wrong because not unchanging)

Enzyme-substrate complex

what forms when (a) substrate(s) binds to an enzyme on its active site

Enzyme-catalyzed reactions are

reversible

Enzyme name

substrate + ase (ex. Sucrase, lactase)

Coenzymes

vitamins that assist enzymes

Cofactors

inorganic molecules that assist enzymes

How is enzyme efficiency impacted by temperature and pH?

Efficiency increases with temperature up to a point, then denaturation begins (human body temp 37C – near-optimal for human enzymes); too high or too low pH causes denaturation; different enzymes have different optimal ranges (ex. Gastric enzymes active at low pH (stomach acid); intestinal amylase optimal in basic/alkaline environment)

Enzymatic inhibition

turn off genes coding for enzymes; regulating once made (competitive, noncompetitive inhibition)

Competitive inhibition

compounds that RESEMBLE the substrate compete for the same active site; reversible OR nonreversible

Noncompetitive inhibition

aka allosteric regulation; inhibitor binds to allosteric site away from active site, causing shape change that inhibits enzyme; some toggle between 2 diff configs (shapes), one active (activator) and other inactive (inhibitor)

Allosteric

of enzymes, change in shape alters efficiency

Feedback inhibition

end product of metabolic pathway is allosteric inhibitor for early step; used to economically regulate lengthy metabolic pathways

Cooperativity

type of allosteric ACTIVATION; binding of one substrate to one active site of one subunit of enzyme causes change in entire molecule and locks ALL SUBUNITS into ACTIVE position; AMPLIFIED RESPONSE OF ENZYME TO SUBSTRATE

If adding more substrate doesn’t affect enzyme inactivity

caused by noncompetitive/allosteric inhibition

Anaerobic respiration

in prokaryotes or eukaryotes when not enough O2 present (ex. exercise); glycolysis, alcoholic/lactic acid -> 2 ATP; ONLY AS LONG AS ENOUGH NAD+, so RESPIRATION REQUIRED TO RESTORE NADH to NAD+

Aerobic respiration

EXERGONIC overall (produces energy ATP); eukaryotes only, happens mainly in mitochondria; glycolysis, CAC, ETC, oxidative phosphorylation -> lots of ATP (36-38)

Reduction

GAIN of particle: electrons or protons (H+)

Oxidation

LOSS of particle: electrons or protons (H+)

Redox reaction

reaction in which ones substance is reduced and the other is oxidized

As hydrogen transferred from glucose to oxygen

it goes to a lower energy level, powering ATP synthesis

ATP

adenosine triphosphate; made up of adenosine (NUCLEOTIDE ADENINE) + ribose (SUGAR) + 3 phosphates; UNSTABLE because all phosphates negatively charged and repel

ADP

adenosine diphosphate; more stable version of ATP caused by loss of one phosphate group and subsequent release of energy

Change from less stable to more stable

always releases energy

Glycolysis

CYTOPLASM; 2 ATP + 1 glucose -> 2 pyruvate + 4 ATP; 10 step process that breaks down 1 glucose to 2 3-carbon pyruvates/pyruvic acid and releases 4 ATP; activation energy is 2 ATP so NET ATP GAIN IS 2 ATP; produced by KINASES phosphorylating ADP directly (substrate level phosphorylation)

Substrate-level phosphorylation

Direct transfer of phosphate via kinases

PFK

phosphofructokinase; allosteric enzyme that catalyzes the 3rd step of glycolysis; inhibited by ATP when concentration great enough, causing change in conformation and stop of glycolysis

Cristae membrane

inner membrane of the mitochondria, folded to increase surface area; ETC and oxidative phosphorylation occur here

Intermembrane space

space between smooth outer membrane and folded cristae membrane in mitochondria; made ACIDIC (high H+ concentration) by oxidative phosphorylation

Matrix

inner compartment of mitochondria; Krebs/CAC occurs here

Parts of cellular respiration

cytoplasm–glycolysis; matrix–krebs cycle; cristae membrane–ETC; intermembrane space–proton concentration builds up

Citric acid cycle

aka Krebs cycle; in mitochondrial matrix; requires ACETYL CoA (= PYRUVATE + CoA); oxidizes glucose to CO2; turns TWICE for each glucose molecule (1/pyruvate) and produces 1 ATP PER TURN through SUBSTRATE LEVEL PHOSPHORYLATION; rest of chem energy transferred to NAD+ and FAD to create NADH and FADH2 (electron carriers -> ETC)

Citric acid cycle products

3 NADH, 1 ATP, 1 FADH, CO2 (waste, exhaled)

Oxidative vs. substrate-level phosphorylation

substrate-level = direct enzymatic transfer of phosphate, produces much less ATP than oxidative phosphorylation

NAD+

nicotinamide adenine dinucleotide; PRODUCES 3 ATP (more) via ETC; coenzyme that carries protons/electrons; oxidized form, reduces is NADH (1 proton + 2 electrons)

FAD

flavin adenine dunucleotide; PRODUCES 2 ATP (less) via ETC; coenzyme that carries protons/electrons; oxidized form, reduced is FADre or FADH2

Without NAD+ to accept protons/electrons

CAC and glycolysis would cease and the cell would die

ETC

electron transport chain; proton pump in mitochondria that COUPLES EXER- (flow of electrons) and ENDERGONIC (pumping of protons) REACTIONS (series of REDOX); establishes PROTON GRADIENT; NO DIRECT ATP CREATION but sets up chemiosmosis; in cristae membrane; O2 final electron acceptor b/c highly electronegative and pulls electron

oxidative phosphorylation

depends on chemiosmosis; oxidizes NADH and FADH2 to phosphoryate ADP into ATP via potential energy stored in proton gradient created by ETC; powered by REDOX REACTIONS IN ETC; protons pumped from matrix to intermembrane space

Chemiosmosis

protons can only flow back into matrix via ATP synthase channels, generating energy to phosphorylate ADP into ATP (like hydroelectric dam)

Ubiquinone

aka coenzyme Q; MOBILE ELECTRON CARRIER

How does the structure of a fluid membrane relate to its function?

If cristae were not fluid, ubiquinone couldn’t flow through it and ETC WOULDN’T OPERATE

Cytochromes

proteins similar to hemoglobin, compose most of ETC

Oxygen in ETC

final electron acceptor because extremely electronegative and pulls electrons through ETC; ½ O2 + 2 electrons + 2 protons = WATER (waste of cell respiration)

Kinase

enzyme that transfers phosphates directly (onto ADP)

Energy flow in respiration

glucose -> NADre and FADre -> ETC -> chemiosmosis -> ATP

Facultative anaerobes

can live with oxygen but don’t use it

Obligate anaerobes

can’t live in environment with oxygen

Without conversion of NADH back to NAD+

glycolysis would shut down (why fermentation follows glycolysis)

Alcoholic fermentation

convert pyruvate from glycolysis to ethyl alcohol and CO2 in absence of oxygen AND OXIDIZE NADH -> NAD+ (yeast: CO2 = breadmaking; alcohol = liquor)

Lactic acid fermentation

convert pyruvate from glycolysis to lactic acid AND OXIDIZE NADH -> NAD+ (dairy industry; HUMAN SKELETAL MUSCLES during strenuous exercise–lactic acid converted BACK TO PYRUVATE in liver once normal O2 levels)

What processes produce exhaled CO2?

Oxidation of pyruvate at end of GLYCOLYSIS and CAC

Photosynthesis

6CO2 + 6H2O -light-> C6H12O6 + 6O2; process by which light energy is converted to chemical energy and carbon is fixed

Photosynthetic pigments

absorb light energy to provide energy to carry out photosynthesis; chlorophylls (a and b), caretenoids (including xanthophyll), and phycobylins

Chlorophyll

photosynthetic pigment; a and b; are green, absorb red, blue, violet

Caretenoid

photosynthetic pigment; are yellow, orange, red, absorb blue, green, violet

Xanthophyll

type of carotenoid with slight chemical variation

Phycobilins

photosynthetic pigment; are reddish, absorb blue, green

Antenna pigments

pigments that capture light in wavelengths OTHER THAN CHLOROPHYLL a (chlorophyll b, carotenoids, phycobilins) to absorb photons and pass to chlorophyll a

Chlorophyll a

magnesium head with DOUBLE BONDS (provide electrons) and hydrocarbon tail; takes energy from antenna pigments to help transform light energy into sugars

Action spectrum

graph with rate of photosynthesis vs. wavelengths of light

Different types of chlorophyll

give a plant greater flexibility to exploit light energy

Chloroplast

grana = stacks of thylakoids (light-dependent); stroma ~= cytoplasm (light-independent/Calvin cycle)

PS I

functions SECOND; P700 (best in 700nm range); reaction center with chlorophyll a, region with antenna pigments to funnel to a

PS II

functions FIRST; P680 (best in 680nm range); reaction center with chlorophyll a, region with antenna pigments to funnel to a

Light-dependent reactions (noncyclic phosphorylation)

light absorbed in PSII to excite electrons in double bonds in chlorophyll a, electrons replaced via PHOTOLYSIS (splitting of water into 2H+ 2e- 1O (waste–turns into O2 then into air); excited electrons captured by PRIMARY ELECTRON ACCEPTOR and flow to PSI (electrons replaced by electrons from PSII) in ETC made of CYTOCHROMES, flow to NADP -> NADPH via H from water; creates ATP via chemiosmosis via ETC, like respiration

Photophosphorylation

chemiosmosis used during light reactions in ETC from PSII to PSI to pump H+ across thylakoid membrane from stroma into THYLAKOID SPACE (LUMEN); H+ flow back to stroma through ATP synthase channels, creating ATP to power CALVIN CYCLE

Light-dependent reactions (CYCLIC phosphorylation)

ONLY TO PRODUCE ATP, NO NADPH OR O2; when chloroplast runs low on ATP; just from P680 to P700 and back again

Light-independent reactions

aka Calvin cycle; REDUCTION reaction that performs CARBON FIXATION and produces 3-C sugar PGAL (phosphoglyceraldehyde); SIX TURNS to make glucose; uses products of noncyclical light reaction (ATP and NADPH); doesn’t need light, but ONLY OCCURS IN LIGHT; CO2 enters, attached to 5-C sugar RuBP (ribulose biphosphate) to form 6-C that immediately breaks down into 2 3-C 3-PGA G3P (3-phosphoglycerate) using rubisco enzyme to catalyze (ribulose biphosphate carboxylase)

C-3 plants

plants in which first step of Calvin cycle produces 3-C sugar 3-PGA (3-phosphoglycerate)

Photorespiration

occurs when RUBISCO BINDS WITH O2 instead of CO2; unlike respiration, NO ATP; unlike photosynthesis, NO SUGAR; peroxisomes break down products of photorespiration; not useful, vestige of ancient Earth when no oxygen to deal with

C-4 photosynthesis

modification for dry environments; minimize water loss and maximize sugar production by PUMPING CO2 AWAY FROM AIR SPACE AND DEEP INTO LEAF BEFORE CALVIN CYCLE; C-4 plants thrive in hot, sunny environments (ex. Corn, sugar cane, crabgrass)

C-4 plant examples

corn, sugar cane, crabgrass

Strategy of plants to minimize water loss

C-4 photosynthesis

Number of turns of Calvin cycle to produce glucose

six

Most and least efficient light for photosynthesis

violet and red most; green least (reflected)

Bromothymol blue

pH indicator: yellow when acidic, blue when basic; in CO2 water, yellow because carbonic acid

Phenolphthalein

pH indicator: clear when acidic, pink when basic; in CO2 water, clear because carbonic acid