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
Four classifications of biochemical reactions?
Group transfer, oxidation/reduction, elimination/isomerisation/rearrangement, making/breaking carbon-carbon bonds
What does a covalent bond consist of?
Electron pair shared (not always equally) between two atoms
1) What two types of covalent bond breakage occurs? Describe!
2) What determines the pattern of this bond breakage?
1) Heterolytic cleavage (electron pair stays with one atom - more common) and homolytic cleavage (one electron stays with each atom -> FREE RADICALS!)
2) Electronegativity (degree to which atom attracts electrons) - upper right periodic table is more electronegative.
Heterolytic cleavage of a C-H bond in methane (CH4) will create which two possible sets of products?
Carbanion (CH3 w/electron pair on C-) and a proton (H+), or a carbocation (CH3 w/C+) and a hydride (H- w/electron pair) [transfer of hydride occurs only directly to electron acceptors like NAD+]
What are nucleophiles and electrophiles?
Nucleophiles: electron rich compounds (typically negatively charged or have unshared electrons pair, and easily form bonds with electron deficient centers)
Electrophiles: electron deficient compounds (typically positively charged or contain unfilled valence shells or contain electronegative atom)
How do the following molecules become nucleophiles?
NB: Also forms electrophiles:
Name some important electrophiles in biochemistry
Protons (H+), metal ions (eg: Mg 2+), carbonyl carbon atom (C becomes electron deficient because electrons are drawn to the double bonded oxygen), cationic imine
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).
Describe redox reactions
Involve the loss and gain (Reduction Is Loss, Oxidation Is Gain) of electrons - two bonding electrons are transferred at once to electron acceptor (eg: NAD+)
What is the ultimate electron acceptor?
Oxygen
Complete this oxidation reaction (alcohol) [General Base + Alchohol + NAD+]
What do eliminations form? Which groups are usually eliminated? What is usually released?
C=C double bonds. Hydroxy or amino groups. H2O or NH3 are released.
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).
What are anabolism and catabolism?
Anabolism: synthesizes complex molecules (eg: enzymes) from more simple building blocks (consumes energy)
Catabolism: break down or oxidation of complex molecules/nutrients (produces energy + metabolically useful intermediates)
What is the end product of the catabolism of CHO, fats, proteins, and oxygen?
Water and carbon dioxide
Fill in the blanks.
What are the three main electron carriers that deliver electrons to the electron transport chain?
What is the main molecule used to ‘store’ the energy?
NAD+/NADH, NADP+/NADPH, FAD/FADH2
ATP
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)
How much energy is gained from splitting ADP to AMP? Why doesn’t this happen?
How much energy grained from splitting AMP to Adenosine?
- 31kJ/mol (doesn’t happen much because we only have one enzyme that does it - myosin kinase)
- 14kJ/mol
Formula for calculating energy released under physiological conditions when ATP is hydrolyzed (ATP + water -> ADP + Pi, delta-G {standard conditions} = ~-31kJ/mol)?
Why is this difficult to measure?
delta-G = delta-G {standard} + R*T*ln([ADP][Pi]/[ATP][water])
T = temp (K)
R = gas constant = 8.31451
(difficult because determining concentrations can be difficult)
When electrons are transferred from nutrient molecules (eg: glucose) to an electron carrier, the nutrients are ______________ and the carriers are ___________________
oxidised (loss of electrons), reduced (gain of electrons)
Oxidation of carbs/fats/etc by oxygen is, in principle, a ___________ (but one that is __________, so as not to just produce ______).
combustion, controlled, heat
Each half-reaction of a redox reaction is linked to a _________/_________ potential (and can be calculated using the ________ equation).
What is the equation?
electrochemical/redox, Nernst
delta-G = -n * F * delta-E (n = electrons transferred, F = faraday constant, delta-E = redox potential)
(NB: positive redox potentials (due to - before n) linked to negative delta-G, so half-reactions with positive potential are spontaneous)
Half-reactions with a more positive redox potential have a stronger _______ potential, whereas more negative ones have a stronger ________ potential
oxidative, reducing
NAD+ + H+ + 2e- <-> NADH {epsilon/redox potential = -0.315}
1/2 O2 + 2H+ + 2e- <-> H2O {epsilon = 0.815}
How do you calculate delta-E for the overall reaction? What is the answer here?
delta-E = Epsilon (acceptor) - Epsilon (donor)
0.815V - (-0.315V) = 1.130V
The electron transport chain consist of many _______ complexes located in the _________ __________ of the ___________. and transfer electrions from ________ ________ to _________. The transport of _________ _____ through these complexes is linked to the production of ___.
Each NADH and FADH2 creates _ and _ ATP respectively.
redox, inner membrane, mitochondria, electron carriers, oxygen, electron pairs, ATP
3, (upto) 2
