molecular cell bio exam 3

1st law of thermodynamics

energy cannot be created no destroyed, only converted

2nd law of thermodynamics

in a closed system, entropy always increases over time —> moving toward disorder

increasing order in the cell generates heat, which dissipates and causes increased disorder outside the cell

3rd law of thermodynamics

as a system approaches absolute zero, all processes cease and the entropy of the system approaches a minimum value

what is energy

capacity to perform work

if a reaction results in a negative change in free energy (-changeG), then the reaction increases disorder and is spontaneous

spontaneous

occurs naturally without continuous input of external stimuli

energy is released (exergonic)

non-spontaneous

requires continuous supply of energy from external sources

energy is consumed (endergonic)

condensation reactions

combines 2 molecules to form single, larger molecule, typically with water expulsion

disaccharide synthesis

dehydration synthesis: non-spontaneous reaction

results in an increase in molecular order (requires energy)

hydrolysis

water breaks a covalent bond, splitting larger molecules into smaller molecules

releases energy (spontaneous)

difference in energy vs direction

X has less energy than Y, favored direction will be toward X

Y—>X

equilibrium

state in which no net changes in the amounts of reactants and products occurs 

both directions of the reaction occur with the same frequency

as reaction proceeds toward equilibrium, entropy increases

free energy change (ΔG)

reflects the degree to which a reaction creates a more disordered state of the universe

(ΔG) < 0 (negative): spontaneous

(ΔG) > (positive): non-spontaneous

(ΔG) = 0: equilibrium 

sequential reactions

total free energy change of the overall process is the sum of the energy changes for each individual step 

breakdown of sucrose

reaction is exergonic (spontaneous) but must go through a high energy intermediate: the bending of the glycosidic bond and requires activation energy

—> glucose and fructose

enzymes

proteins that act as a biological catalyst by accelerating specific chemical reactions 

can lower the activation energy of a reaction and increase rate of reaction

enzyme vs equilibrium point

enzymes speed up rate of a reaction but does not change the equilibrium point

function of enzymes

enzymes catalyze chemical transformations in both directions

ATP (phosphoanhydride bonds)

high energy bonds between the phosphate groups in ATP are the phosphoanydride bonds 

ribonucleotide, energy carrier (source of useful available energy), stores energy

energetically favorable reaction

spontaneous chemical process where the products are more stable and have lower free energy than the reactants -ΔG

energetically unfavorable reactions

non-spontaneous chemical process resulting in a net increase in free energy +ΔG

energy molecules

ATP is an energy carrier molecule, contains ready to use energy

respiration (energy molecules)

harvesting of the energy stored in macromolecules

oxidation of sugars

catabolic reactions (respiration)

breakdown of food molecules into basic components

their energy is released and transferred to carrier molecules 

anabolic reactions (biosynthesis)

use of products of food breakdown as building blocks for the synthesis of necessary macromolecules

requires energy from energy carriers

respiration (breathing)

breakdown of sugars and energy storing molecules

consumes oxygen

releases cos and water

photosynthesis

energy from sunlight is used to build sugars

carbon obtained from co2

water consumed and oxygen released 

harvesting energy from sugars

slow burning: gradually releasing small pockets of energy

activation energies are lowered by enzymes

oxidation

reaction where molecules loses electrons 

energetically favored

reduction

reaction where molecule gains electrons

energetically unfavorable 

glucose has how many carbons?

6

glycolysis phase 1: investment glucose reaction

glucose (6c) —→ glucose 6-phosphate (6c) through

1. phosphorylation with ATP consumed

2. isomerization to fructose 6-phosphate (6c)

3. phosphorylation with ATP consumed to fructose 1,6-bisphosphate (6c)

glycolysis phase 2: cleavage

4. cleavage —→ glyceraldehyde 3-phosphate (3c) + dihydroxyacetone phosphate (DHAP, 3C)

5. isomerization of DHAP —→ (2) glyceraldehyde 3-phosphate (3c)

glycolysis phase 3: payoff

6. oxidation with 2NAD⁺ reduced to 2NADH and an inorganic phosphate (P_i)—→ (2) 1,3-biphosphoglycerate (BPG, 3C)

7. ATP synthesis by substrate with transfer of 1P from BPG to ADP —→ (2) 3-phosphoglycerate (3c)

8. isomerization —→ (2) 2-phosphoglycerate (3c)

9. dehydration with 2H2O removed —→ (2) phosphoenolpyruvate (PEP, 3C)

10. ATP synthesis by substrate with transfer of 1P from PEP to ADP —→ (2) pyruvate (3c)

glycolysis: yield

2 ATP consumed at the energy investment phase

4 ATP and 2 NADH produced at the energy generation phases 

net yield": 2 ATP + 2 NADH

3 types of muscle fiber

1. slow muscle fiber: appear dark red b/c of high-density myoglobin and generate their ATP in the mitochondria by oxidative phosphorylation

2. intermediate muscle fiber: do both

3. fast muscle fiber: generate ATP by anaerobic respiration

fermentation: anaerobic respiration end products

absence of oxygen

pyruvate is reduced, driven by the oxidation of NADH from glycolysis and getting 2 end products: lactic acid / ethanol + co2

fermentation leading to lactic acid

pyruvate (3c) —→ reduction, NADH oxidized to NAD⁺ —→ lactic acid (3c)

fermentation leading to ethanol and co2

pyruvate (3c) —→ hydrolysis, co2 produced —→ acetaldehyde (2c) —→ reduction, NADH to NAD⁺ —→ ethanol (2c)

aerobic respiration

pyruvate and NADH go to the mitochondria

pyruvate reacts with the coenzyme A, converted too acetyl coenzyme A, centers the citric acid cycle

NADH powers the oxidative phosphorylation reactions (electron transport chain)

mitochondrion

membrane enclosed organelle that is found in most eukaryotic cells, generates most ATP

the matrix is the site of the oxidation of pyruvate and citrus acid cycle

the inner membrane is the site of electron transport chain

the cristae are infoldings of the inner membrane and contain intermembrane space inside

oxidation of pyruvate

pyruvate: (3C)+CoA

oxidation: CoA-SH + pyruvate —→ acetyl CoA + CO2

CO2 is lost and the intermediate is oxidized 

NAD+ is reduced to NADH

Acetyl coenzyme A

the thioester bond in acetyl coenzyme A releases a large amount of energy when hydrolyzed

citric acid cycle overview (kreb’s cycle/TCA cycle)

2 carbons from acetyl CoA that enter the cycle will not be converted to CO2 in this turn, but will convert in later cycles

the 2 carbons that weren’t converted in the previous cycle will be converted to CO2 now

citric acid cycle step 1: condensation

acetyl CoA (2C) + oxaloacetate (4C) —→ citric acid (citrate, 6C) 

driven by the hydrolysis that removes CoA-SH

citric acid cycle step 2: isomerization

citric acid (