Scholz: Bioenergetics Flashcards
What is energy?
The capacity for Work (W) - it is a dynamic state related to change, whose presence emerges when change occurs.
What is the SI unit for energy?
The Joule
How many calories in a joule? What does each calorie represent?
4.184J (energy needed to heat 1g water by 1 degree C).
What is potential and kinetic energy? If you can, give examples.
Potential energy bound in a certain form (but which isn’t necessarily present or visible - for example energy in packaged food, stored in the bonds of the nutrients. Kinetic energy means the energy becomes apparent to cause a change in the system (eg: energy being transferred from ATP in order to drive muscle movement).
Give some forms (6) of energy.
Chemical (combustions, batteries, etc), mechanical (moving/turning masses), heat, light, electric, nuclear
1) What types (2) of mechanical work occur in our bodies? 2) What type of chemical work occurs in our bodies? 3) What types (2) of transport work occurs in bodies? 4) What types (2) of electrical work occurs in bodies?
1) Muscle contraction & cell division 2) Synthesis of molecules (eg: precursor -> squalene -> steroid) 3) Diffusion and active transport 4) Charged particle transport & action potentials in nerves and muscles.
Is energy conversion 100% efficient? Why/why not?
No - they always include the release of waste heat
What is the first law of thermodynamics?
Energy can not be created or destroyed, but is transformed from one form to another without being destroyed.
What is the second law of thermodynamics?
All energy transformations ultimately increase the entropy (disorder/randomness) of the universe.
Building and maintenance of living organisms involves decreasing entropy. How does this work considering the second law of thermodynamics?
No conversion is 100%, so a portion of the energy is always lost as heat (which causes more randomness in the universe as a whole, even if the entropy of the system/organism is reduced) [eg: Fridge - order created inside, heat pumped outside]
What is Gibbs Free Energy?
The energy that can be used by an organism
How is total energy calculated?
Total = useful energy (Gibbs) + non-useful
H (enthalpy) = G (Gibbs) + T (Temp) * S (Entropy) [G = H - T*S]
In a spontaneous process, a system…
… gives up energy (decrease in H/Enthalpy) and/or becomes more random (S/entropy increases) [… has a negative delta-G]
1) A reaction reaches equilibrium when…
2) What is delta-G at equilibrium?
1) … the rate of the forwards reaction equals the rate of the backwards reaction.
2) Delta-G = 0
1) In terms of equilibriums, the sign (+/-) of delta-G indicates… 2) The size of delta-G is an indication of…
1) … on which side of the equilibrium the reactant concentrations lie at a particular time (< k = -G, >k = +G) 2) … how far from the equilibrium the reaction is.
What is a coupled reaction?
A reaction with a sufficiently negative delta-G driving another reaction with a positive delta-G
Do living organisms reach equilibrium?
No (until they die) - they are open systems, taking in high enthalpy low entropy food, and excreting low enthalpy high entropy waste products.
If living organisms can’t reach equilibrium, what is the name of the system we do use? Give an example.
Dynamic steady state systems (oxygen consumption - if we need more, to do activity, we increase intake)
What is the mode of action of enzymes? What do they allow for?
Lock-and-key mechanism (formation of enzyme-substrate complex) - allows for lower temperature and neutral pH conditions whilst still managing to achieve goals
What do enzymes reduce in a reaction?
The activation energy (reduces the free energy of the transition stage, leading to faster reactions, occurring at lower temperatures and neutral pH) NB: applies to both forward and backward reaction, which means equilibrium does not change
How do the following molecules become nucleophiles?
NB: Also forms electrophiles:
What happens when the following nucleophiles/electrophiles react? [3 steps]
NB: Result is imine (doesn’t stick around for long as it reacts with water)
What is a group transfer reaction?
Transfer of electrophilic group from one nucleophile to another
Group Transfer Reactions (Phosphoryl group transfer - the hexokinase reaction). Draw what happens (inc. intermediate step).
Complete this oxidation reaction (alcohol) [General Base + Alchohol + NAD+]
What does isomerization involve? Rearrangements?
Draw out the (electron) shifts that change an aldose into a ketose:
Intramolecular shift of hydrogen to change the location of the double bond. Rearrangements are isomerization reactions that produce altered carbon skeletons.
What are the most common electrophiles and nucleophile used for C-C bond formation?
Electrophile carbonyl group of aldehydes, ketones (see pic), esters, or CO2. Nucleophile = stabilized carbanion (eg: methane that has lost one H, carbon has kept both electrons)
Just study this picture of aldol condensation. Describe what is going on.
Base attacks hydrogen of first ketone. This creates a resonance hybrid (which is stablized because the electrons are hopping between the two double bonds - or rather, both bonds are somewhere between single and double). This then leaves the carbanion to attack another ketone, which it then forges a bond with.
Decarboxylation: what occurs after this step? [Pictured: B-keto acid]
Forms carbanion (resonance stabilized structure) until it can be used for some other purpose. This is done by using the carboxy group as an escape group (sometimes our bodies add a CO2 to do just this - like fatty acid synthesis).
Fill in the blanks.
What happens during the hydrolysis of ATP? How much energy is released?
Nucleophilic attack by water on phosphorus of phosphate group, electrons move towards O connecting to rest of molecule, and phosphate group is broken off (~31kJ/mol)
Why does the hydrolysis of of ATP release so much energy? [3]
- Electron density in the anhydride bonds (X-O-H + X-O-H -> X-O-X + water) between phosphates and on double bonds - splitting some of those away creates a more energy favorable situation (less energy in a small space)
- Negative charges in close proximity repel each other - getting rid of some of these charges is energetically favorable).
- [Main one] Resonance stabilization of inorganic phosphate (electrons blurred/shared between two 1.5x bonds, like in benzene rings [delocalized]]) = more energy can be released (because it gives the other phosphate a chance to achieve greater stability)
