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What is an example of high quality energy?
Potential energy like a mass on a pulley
What is an example of low quality energy?
Heat
What kind of energy conversion do living organisms do?
Convert high-quality energy into low-quality energy
What does energy quality depend on?
How much is “free'“ or available to do work. Can be shown by the Gibbs free energy equation: G=H-TS
What determines whether a process occurs spontaneously?
The change in free energy. delta G<0
How can you build things because the entropy goes down?
Must be coupled to -G reactions
How are free energy values standardized?
They are all measured under the same conditions - standard free energies are additive
How do cells create order?
Couple ATP hydrolysis to create order. As long as the two reactions that are coupled and the -G is larger, the reaction can happen
How can ATP binding/hydrolysis cause changes in proteins and their energy?
Can distort the 3D structure. Free energy has been minimized in the folding of the protien - any deviation from the fold requires energy. Energy has been stored in the protein in the form of strain proteins can relax back into energetic minimum and go back from being strained.
What do redox reactions provide a basis for?
Energy transduction - fuels are oxidized by metabolic enzymes. Electrons released by metabolic processes are one of the main energetic carriers
What is the principle electron acceptor in metabolic redox reactions?
NAD+ it absorbs electrons to make NADH which has positive delta G. The release of electrons is enough delta G to make it happen. NAD+ is positioned precisely to catch the electrons
What does GAPDH do?
Bring NAD+ into position to be reduced
When is FAD used?
When the available free energy could not reduce NAD+
Does NAD+→ NADH or FAD to FADH2 have a cell harvest from a reduction reaction?
NAD+ (52.6 kcal/mol) and FAD: 43.4 kcal/mol
How much energy is available when ATP is hydrolyzed?
-7.3 kcal/mol
What can serve as a baseline for cellular energy scales?
Thermal energy
What is the average kinetic energy in water and what is the formula for it?
Water is in constant motion and their random kinetic energy is heat. Average kinetic energy = 3/2 KB T
KBT= 0.6 kcal/mol
Why do molecules move continuously?
Brownian motion - proteins are in a constant state of motion, diffusion and random motion is because it bumps into different particles in the cell
What is D?
Diffusion coefficient - it is a function of the size of the molecule. Faster diffusion means larger D
What can describe Brownian motion?
Random walk
Where do you get on average from Brownian motion?
Nowhere even though it explores a lot of space. It can be modeled by mean squared displacement
What types of mechanical forces can cells and subcellular structures dell and produce?
Protein filaments pushing against plasma membrane (microtubules) cells can bind to the bottom of a petri dish and pull up on it.
What are the magnitudes of cellular forces?
Measured in pN and nN
What is the force of ATP hydrolysis?
20 KBT or 80pN nm
What is the equation for measuring energy for cells and photons?
E=hv where h=planck’s constant and v= frequency in Hz. A visible photon is 2eV and 80KBT
The surfaces of proteins contain many charged residues what is the equation used to see how much energy to pull another protein with complementary charges?
Coulombs law: E= F=k∣q1q2∣r2
Why is calculating how strong a non-covalent bond like a hydrogen bond difficult?
Need to know the local environment, non-covalent bonds are stronger than thermal energy - thermal energy alone is insufficient to break them apart
How are non-covalent bonds and electrostatic bonds every broken?
The energy of a molecule fluctuates. There is an equation with P for the probability that a particular collision between 2 proteins in solution will reach a specific energy 1/20 collisions can break a hydrogen bond. H bonds don’t last very long
How do you ever make it over a transition state?
Thermal energy alone can provide the energy with some probability. Water in the solution will give enough energy to drive the reaction forward
Can covalent bonds break in the same way?
A collision breaks a covalent bond every septillion years
Do cells have to worry about all types of forces?
yes, at a nanometer thermal energy, electrostatic, and mechanical etc can all converge which is at cell scale
What can ATP hydrolysis be compared to in currency?
$20 bank note - can do stuff but small enough to avoid too much waste
