ap bio u3

definitely contains more info than what's necessary for the ap test

why are organic molecules called "fuel molecules?"

why are organic molecules called "fuel molecules?"

they hv weak cov bonds, so they require lots of energy to stay together -> are rich sources of chemical energy

metabolic pathway

series of chemical reactions in which molecules are broken down or built up

what is ATP

a molecule that contains energy in its chemical bonds

where's ATP come from

as large molecules (w lots of CE) -> smaller molecules (less CE), chemical energy is released & packaged by cells into ATP

fuel molecules (lots of PE) -> ATP -> drive cellular processes

chemical structure of ATP

triphosphate + adenine + 5 carbon sugar (ribose)

wheres the accessible chem energy of ATP held? and why?

btwn bonds connecting phosphate groups

the bonds have high PE because they repel (neg charges) so when new bonds r formed, the excess is released

1st law of thermodynamics

energy cannot be created or destroyed, only transformed

2nd law of thermodynamics

every energy transfer increases the entropy (or disorder) and becomes less efficient (less energy available for use)

whats adding energy do to the order of a system

adding energy -> increase order of system

how do cells/organisms remain so organized despite all the energy transfers/transformations?

they're made up of many parts, so the heat can be released in the surrounding environment (aka entropy increases outside of the cell/organism)

gibbs free energy + equation

amt of available energy to do work

ΔG = products - reactants

endergonic/exergonic

ender: POS ΔG (REQUIRES ENERGY, NONSPONTANEOUS)
exer: NEG ΔG (RELEASES ENERGY, SPONTANEOUS)

ATP hydrolysis

ATP -> ADP + Pi

released energy from forming more stable bonds fuels other processes

exergonic (neg ΔG)

energetic coupling

a spontaneous reaction drives a non spontaneous reaction
- sum of ΔG must be neg & they must occur tgt (sometimes shares a common molecule)

enzymes

protein catalysts in cells

transition state

a high-energy/unstable intermediate state where old bonds are breaking and new ones are being formed

how do enzymes work? (4 steps)

-> binds to reactants
-> forms complex which stabilizes transition state
-> reduces Ea
-> proceeds quicker

provides an alternative pathway that makes it more likely for reaction to proceed

enzyme-substrate complex

E + S => ES => EP => E + P

S: substrate
E: enzyme
P: product

active site + types of bonds formed

the region of the enzyme where substrates are bonded to

- transient (v temporary) covalent bonds
- more commonly, noncov interactions (ionic, h-bonds, VDW)

what does the active site do?

substrate binds to it and it converts substrate to product

with more than one substrate, the active group aligns them & restricts their motion to increase probability of product creation

two models for binding of substrate?

lock & key + induced fit

lock & key model

enzymes are SPECIFIC for certain substrates

induced fit model

shape of active site is modified bcs substrate & active site are able to mold to each other

what happens to enzymes @ low & high temps

low temps: molecules move slower w less KE => reduces probability that reactants interact w enzymes

high temps: enzyme will unfold/denature & loses catalyzing abilities

chaperone proteins

proteins in cells that help protect slow-folding or denatured proteins until they attain proper structure (tho most happen super fast)

2 ways pH impacts enzymes & how

charges of amino acids:
=> lower pH (lots of H+): protons bind to functional groups (increase in + charges)
=> higher pH: the opposite (increase in - charges)

overall shape (protein folding):
changes amino acid charges and thus amino acid interactions as shape is formed

activators & inhibitors

compounds that increase activity of enzymes, decrease activity of enzymes

irreversible & reversible inhibitors

irreversible: forms cov. bonds & irreversibly inactivates enzymes

reversible: forms weak bonds & easily dissociates from enzymes

competitive inhibitors

binds to active site of enzyme (similar in structure w substrate)

SOLVED BY INCREASING SUBSTRATE CONCENTRATION

noncompetitive inhibitors

binds to different site (allosteric site) and therefore changes the shape & activity

CANNOT BE SOLVED BY INC. SUBSTRATE CONC.

allosteric enzymes

enzymes that are regulated by molecules that bind @ other sites (not active sites)

photosynthesis

using sunlight to turn H2O and CO2 into carbs (glucose)

NADPH/NADP+

a type of electron carrier in cells

oxidized: NADP+ (decrease in H cov. bonds)
reduced: NADPH (increase in H cov. bonds)

(NADP+) + (2e-) + (H+) => NADPH
*and vice versa

photosynthesis is a redox reaction

carbon partially gains e- (6CO2 => C6H12O6)
oxygen partially loses e- (6H2O => 6O2)

the two stages of photosynthesis

light reactions and calvin cycle

light reactions (light dependent)

1. chlorophyll absorbs sunlight energy
2. electrons move along photosynthetic electron transport chain
3. NADPH & ATP is produced

inputs: ADP, water, NADP+
outputs: ATP, O2 (g), NADPH

calvin cycle (light "independent")

CO2 -> carbs

*doesn't DIRECTLY use sunlight, but still needs it for the ATP & NADPH

where does each part take place?

light reactions: thylakoids (stacks = grana)
calvin cycle: stroma

pigments

absorbs some wavelengths of visible light

chlorophyll

the major photosynthetic pigment (entry point for light)

*has two types: chlorophyll a &b

chlorophyll within an intact chloroplast in a lab vs in a cell

in lab: absorbed light energy is released (and chlorophyll then returns to ground state)

in cell: energy is transferred to an adjacent chlorophyll molecule (very little energy is lost as heat)

antenna chlorophyll

the chain of chlorophyll molecules where energy is transferred

reaction center

includes a pair of chlorophyll a molecules that accept & lose e'

When excited, the reaction center transfers an electron to an adjacent molecule that acts as an electron acceptor. When the transfer takes place, the reaction center is oxidized and the adjacent electron-acceptor molecule is reduced. Once the reaction center has lost an electron, it can no longer absorb light or contribute additional electrons. Thus, another electron must be delivered to take its place. These electrons come from water.

photosystems

protein-pigment complexes that absorb light energy & drive electron transport

flows from photosystem II -> photosystem I

photosystem II

energy captured by II allows electrons to be pulled from water

photosystem I

energy captured by I allows electrons to be transferred to NADP+ to form NADPH

three sections of the Z scheme (photosynthetic electron transport chain)

light energy is first absorbed to pull electrons from H+

what r the ways protons accumulate inside thylakoid

from oxidation of water

as e- move along chain, protons are pumped from stroma -> thylakoid

proton gradient/electrochemical gradient

SOURCE OF POTENTIAL ENERGY (STORES IT) bcs thylakoid wants to go to stroma (except membranes r only selectively permeable)

chemical vs elec gradients

chem gradient: diff in concentrations btwn sides of membrane
elec gradient: diff in charges btwn 2 sides of membrane

ATP synthase (general & specific idea)

ATP synthase uses light energy to synthesize ATP

enzyme that uses KE from proton movement down electrochem gradient (from thylakoid => stroma) to synthesize ATP

ADP + Pi => ATP

photophosphorlyation

(light energy powered) process by which phosphate is added to a molecule (ADP + Pi)

entire process (sunlight-> synthesizing atp)

sunlight energy is absorbed by a chlorophyll (a/b) and the energy is passed btwn chlorophylls inside PS II.

electron eventually reaches the reaction center (contains special pair of c.a). the electron is then transferred to primary electron acceptor

so, H2O is added to final chlorophyll RC to reduce it.

meanwhile, electron travels down photosynthetic ETC (releases H+ as it goes) till it reaches PS I where electron loses energy (light energy then gives it energy again)

also in PS II, water also releases H+ and O2 (along with the e-)

the H+ from the past two steps travel down concentration gradient thru ATP synthase to combine with ADP to form ATP

the e- in PSI travels down its own ETC and electron is released where it binds with NADP+ to form NADPH

the calvin cycle (occurs in light y/n?)

series of enzymatic reactions that synthesize carbs from CO2

(doesn't directly use sunlight, but needs NADPH & ATP => only occurs in the light)

1. carbon fixation + catalyzed by what?

CO2 in air is converted to organic molecule in a cell

CO2 + RuBP (5-carbon molecule) = 6-carbon molecule
=> breaks into two 3-carbon molecules

*catalyzed by rubisco

2. reduction

3-carbon molecules => carbs (triose phosphates/G3P)
*requires ATP & NADPH

triose phosphates/G3P

true products of calvin cycle & principal form of carbs exported from chloroplast during photosynthesis

(later converted into glucose)

*CYCLE MUST REPEAT 6 TIMES BCS EACH CYLE ONLY ONE G3P IS RELEASED

3. regeneration

G3P + 3 ATP => regenerate 5-carbon sugar (RuBP)

*requires ATP

what happens to the excess carbs (G3P) that's produced + two benefits

converted to starch (storage form of carbs) through dehydration synthesis

=> stored in granules that aren't water soluble (doesn't lead to osmosis)
=> provides photosynthetic cells w source of carbs during night

substrate

reactant of an enzyme-catalyzed reaction

THING THAT ATTACHES TO ENZYME

photorespiration

rubisco adds O2 to 5-carbon molecule => CO2

*ATP is consumed = net energy drain
*oxidizes and loses carbon atoms

why does photorespiration still happen then?

due to the similar in size & structure of CO2 and O2, rubisco struggles to distinguish between them

to increase its selectivity for CO2, its reaction speed is slower
=> rubisco must be produced in large quantities

however the abundance of O2 in atmosphere means photorespiration still causes loss of carbon

what happens if light reactions proceed quicker than calvin cycle

NADP+/ADP will be in short supply, electron transport chain backs up (excess e- and energy)

=> creates reactive oxygen species (can cause substantial damage to cell by oxidizing macromolecules)

*most likely under high light intensity (such as midday)
*cold temperatures reduce rate of NADPH/ATP production (and increases ROS production)

how do photosynthetic organisms avoid stresses that arise from calvin cycle not being able to keep up??!

chemicals that detoxify ROS: exists in high conc in chloroplasts

prevent ROS from forming at all:
ex. xanthophylls (reduces excess light energy by converting it to heat)

cellular respiration

metabolic pathway that converts energy in carbs/fuel molecules => chemical energy in ATP

SYNTHESIZE ATP FOR USE BY CELL

cellular respiration overall reaction

glucose + oxygen -> co2 + water + energy

what's oxidized and what's reduced in cellular respiration?

oxidized: C6H12O6 => CO2
(carbon goes from equally shared to all towards EN oxygen)

reduced: O2 => H2O
(equal sharing => gained electrons go towards EN oxygen)

two ways of ATP production

substrate-level phosphorylation
1. hydrolysis of molecule to yield phosphate group
2. addition of P group to ADP (from enzyme substrate)

oxidative phosphorylation
1. energy transferred to electron carriers (NAD+ & FAD)
2. they each gain 2 e- from the oxidation of fuel molecules
*driven by pumping of protons (electrochem gradient)
*oxygen is final electron acceptor & produces water

whys cellular respiration necessary?

1. tho photosynthetic organisms make their own carbs, they need ATP bcs its cell's usable & ready form of energy
(ATP produced during photosynthesis is for calvin cycle)

2. used at night when theres no light energy to make ATP

photosynthetic vs respiratory ETC (energy & location)

P: harnesses sunlight energy
R: harnesses energy from fuel molecules

P: in thylakoid membrane
R: located in inner membrane of mitochondria

4 stages of cellular respiration

glycolysis, pyruvate oxidation, krebs cycle, oxidative phosphorylation

1. glycolysis (action, products, location)

ACTION: glucose is broken down to pyruvate
PRODUCTS: 2 ATP (4-2), 2 NADH, 2 pyruvate
LOCATION: in cytoplasm

glycolysis initial reactants & final products

initial: 6-carbon molecule of glucose
products: two 3-carbon molecules of pyruvate

NET TOTAL: 2 ATP & 2 NADH
*directly thru SLP

phase 1 of glycolysis + why?

preparatory phase: adds 2 phosphate groups to glucose
1. confines product of reaction to INSIDE the cell
2. neg charged P groups repel & destabilized molecule so it can be broken apart (in stage 2)

REQUIRES ENERGY (ENDERGONIC)
=> 2 ATP is used per molecule of glucose

phase 2 of glycolysis

cleavage phase: 6C molecule => two 3C molecules

phase 3 of glycolysis

payoff phase: 4 ATP, 2 NADH, and two molecules of pyruvate are produced

2. pyruvate oxidation (action, products, location)

ACTION: pyruvate is oxidized to acetyl-coenzyme A (acetyl-CoA)
PRODUCTS: 2 NADH, 2 acetyl-CoA, 2 CO2
*co2 = waste, NADH forms from NAD+ and e- lost by pyruvate

LOCATION: mitochondria

acetyl group (COCH3)

transferred to coenzyme A (CoA) which carries acetyl group to next step

(contains large amt of PE)

3. krebs cycle/citric acid cycle (action, products, location)

ACTION: acetyl group oxidized to CO2, free energy is transferred to ATP (SLP)
PRODUCTS: 2 ATP, 6 NADH, 2 FADH2, 4CO2
LOCATION: mitochondrial matrix

*PRODUCES MUCH MORE ENERGY THAN IN STAGES 1 & 2

first part

2C acetyl-CoA + 4C oxaloacetate = 6C citric acid

second part

four redox reactions produce three NADH & one FADH2

these carriers donate e- to ETC

third part

citric acid is oxidized in series of reactions where the last reaction regenerates 4C oxaloacetate (joins 2C and cycle continues)

4. oxidative phosphorylation (action, products, location)

ACTION: FADH2 & NADH donate e- to respiratory ETC
PRODUCTS: ATP, H2O, NAD+ & FAD
LOCATION: inner mitochondrial membrane

*PRODUCES THE MOST ATP

respiratory ETC is made up of

four large protein complexes (complexes I to IV) embedded in inner mitochondrial membrane

donated electrons enter where? what happens to them?

donated by NADH: complex I
donated by FADH2: complex II

(then transported thru III and then IV) => OXIDIZED

redox couples

within each protein complex, e- is passed from e- donor to acceptor (redox centers)

oxidized & reduced form = redox couple
eg. oxygen accepting e- in the presence of H+ is reduced to H2O

proton gradient is caused by?

caused by oxidation of NADH & FADH2

how does proton gradient help (3 steps)

proton flow thru transmembrane protein makes it possible for ATP synthase to create ATP

1. proton gradient makes channel rotate
2. PE is converted into KE (mech rotational energy)
3. enzyme changes shape which allows it to ADP -> Pi

chemiosmosis

protons moving across membrane + synthesis of ATP

how much ATP produced for each NADH & FADH2 (that donates e- to the chain)?? total ATP produced?

NADH: 2.5 molecules
FADH2: 1.5 molecules

OVERALL: 38 molecules of ATP from all 4 stages of CR

uncoupling agents

protons that spanning inner membranes that allow protons to bypass ATP synthase channel
=> decrease proton gradient & levels of ATP
=> energy of proton gradient is dissipated as heat

*found naturally for heat generation, also are poisons

what types of reactions lead to production of ATP & reduced e- carriers

exergonic reactions (no outside energy necessary, decrease in free energy)

how is excess glucose stored?

glycogen in animals, starch in plants

other molecules that can produce ATP are?

oxidizing fatty acids can provide a large amt of ATP, BUT can't be used by all tissues of body (ex. RBC's and the brain)

proteins broken down to amino acids enter at various points in stages 1-3, but are a last resort energy source bcs they hv other roles (structural, etc.)

what happens after glycolysis in anaerobic respiration?

concentration of pyruvate builds up in cytoplasm

how can the pyruvate be broken down then/how can NAD+ be regenerated?

fermentation: metabolic pathways that extracts energy from fuel molecules w/ out O2 or ETC

whens fermentation used

organisms w out oxygen, for yeast/others that favor fermentation, and also when oxygen cant be delivered quickly enough (eg. exercise)

lactic acid fermentation

e- from NADH are transferred to pyruvate

Glucose + 2 ADP + 2Pi => 2 Lactic acid + 2 ATP + 2H2O

bacteria & animals (yeast)

ethanol fermentation

pyruvate releases CO2 => acetaldehyde
acetaldehyde + e- (from NADH) => ethanol & CO2

Glucose => Ethanol + 2CO2 + ATP

plants and fungi (muscles)

ATP yield of fermentation

2 molecules of ATP
(end products aren't fully oxidized and still contain large amts of chemical energy => LOTS OF FUEL MOLECULES ARE NECESSARY TO POWER THE CELL)