biochem & nutrition exam 1 Flashcards
1st and 2nd law of thermodynamics
first law: total amount of energy in the universe is constant, but forms change - energy can be transferred but not destroyed
second law: in natural processes, entropy tends to increase
What makes a reaction go? Energetics/Thermodynamics
enthalpy (H): number & type of chemical bonds
the net change in enthalpy, delta H, for a rxn depends on the relative strengths of the bonds broken and formed
delta H < 0 (so negative): heat generated/released - bond broken so hot
delta H > 0 (so positive): heat energy transformed - bond formed so cold
measured in kilojoules per mole (kJ/mol)
Calculate the enthalpy change of a reaction:
Sum Enthalpy (Products) minus
Sum Enthalpy (Reactants)
Energetics/Thermodynamics
entropy (S)
As time moves forward, the net entropy (degree of disorder) of any isolated or closed system will increase. It takes a lot of effort (energy?) to decrease entropy.
measure of randomness
delta S > 0: system becomes more random, less ordered
delta S < 0: system becomes less random, more ordered
Energetics/Thermodynamics
Gibbs Free Energy (G) is the available energy in a system to do work.
Gibbs free energy
delta G < 0: exergonic, rxn released energy - destroy, catabolic
delta G > 0: endergonic, must put in energy into the system to make the reaction happen - building, anabolic so the energy required
exergonic vs endergonic
delta G < 0: exergonic: products predominate at equilibrium (‘occurs spontaneously as written [left to right]
delta G > 0: endergonic: reactants predominate at equilibrium (‘does not occur spontaneously as written [ occurs spontaneously in reverse direction)
delta G = delta H - TdeltaS
factors that contribute to making delta G more negative (less positive):
- negative delta H (exothermic rxn)
- positive delta S (increasing entropy [more random])
factors that contribute to making delta G more positive (less negative):
- positive delta H (endothermic rxn)
- negative delta S (decreasing entropy [more random])
equilibrium
is not a state where there are equal concentrations of all reactants and products
it is a state where [ ] remains constant. Those concentrations have to be determined experimentally. Then an equilibrium constant can be calculated, and from this, the delta G knot can be calculated.
completion depends on a specific set of concentrations determined by an equilibrium constant Keq
completion depends on a specific set of concentrations described by an equilibrium constant Keq
Keq
= concentration products/concentration reactant
one can compare where the reaction is going when you use Q and compare it to Keq, given the concentrations of all of the constituents
Q > K = more products, net rxn to the left
Q = K = equal [ ] of products and reactants, no net rxn
Q < K = more reactants, net rxn to the right
will a rxn occur under actual conditions? the answer depends on delta G, not just delta G knot
this means that delta G changes based on concentrations of reactants/products
K’eq > 1.0, delta G’ knot is negative, starting with all components at 1M the reaction proceeds forwards
K’eq = 1.0, delta G’ knot is zero, starting with all components at 1M the reaction is at equilibrium
K’eq < 1.0, delta G’ knot is positive, starting with all components at 1M the reaction proceeds reverse
IF: Keq > 1, ∆G° is large and negative→meaning?
IF: Keq < 1, ∆G° is large and positive→meaning?
IF: Keq > 1, ∆G° is large and negative→meaning? - move forward, to right
IF: Keq < 1, ∆G° is large and positive→meaning? - move reverse, to left
thermodynamics of biosystems
left alone (w/o any energy input), biosystems would fall apart (entropy maximization)
to maintain order, and to grow, energy input is required
to accomplish this, exergonic rxns are coupled to endergonic rxns
Metabolism: The sum total of all chemical reactions in an organism. Metabolism = Anabolism + Catabolism
Anabolism: Synthetic reactions. Normally endergonic (+∆G)
Usually involves reduction (Entropy = negative)
Catabolism: Degrative Reactions Normally exergonic (-∆G)
Usually involves oxidation (Entropy = positive)
catabolism & anabolism
often just the reverse of each other
but at least one step is catalyzed by different enzymes in different directions
one step is often thermodynamically greatly favored in one direction
the two processes often take place in different parts of the cell
catabolism & anabolism
synthesis of complex molecules and many other metabolic rxns required energy (endergonic)
- thermodynamically unfavorable rxns (delta G’ knot > 0) create order and require work and energy
higher energy barriers (delta G railroad tracK) exist for many stable metabolites (ex: sugar)
breakdown of some metabolizes releases significant amount of energy (exergonic)
- such metabolites (ATP, NADH, NADPH) can be synthesized using energy from sunlight fuels
Reaction Coupling
Some reactions are not energetically favorable. The first reaction of glycolysis, for example, wants to go in reverse.
ex:
glucose to glucose-6-phosphate is coupled to ATP hydrolysis
In living organisms, an energy-releasing reaction can be coupled to an energy- requiring reaction to drive the otherwise unfavorable reactions.
more thermodynamics
ordinarily, less than 100% of the released energy is transferred in a pair of rxns
recall that enzymes change rates, not delta-G
standard delta G’s are additive
Reaction Coupling
High-energy compounds are used by all organisms to provide a driving force for thermodynamically unfavorable reactions (entropy).
Two reactions are “coupled” when one reaction is energetically favorable and can provide energy which allows the second reaction (unfavorable on its own) to occur.
How does this work?
The ∆G values of sequential reactions are additive!
So: (1) Glucose + Pi → glucose 6-phosphate + H2O ∆G1 = 13.8 kJ/mol (2) ATP + H2O→ ADP + Pi ∆G2 = -30.5 kJ/mol
Sum: ATP + glucose → ADP + glucose 6-phosphate ∆GTOT = -16.7 kJ/mol
The energy released by the second reaction drives the first reaction!
Thermodynamically unfavorable reactions (anabolic?; ∆G > 0) create order and require work and energy. We gotta get that energy from somewhere.
Energy Releasing Reaction? ATP and other compounds!
molecules that contain a phosphate tend to have more energy than the same molecule without the phosphate
for instance, adding phosphate to glyceraldehyde (via the hydrolysis of ATP) will yield. a higher energy molecule called glyceraldehyde 3-phosphate (GAP)
Energy Releasing Reaction? ATP and other compounds!
All 3 phosphate groups are negatively charged and the like charges of the phosphate repel each other
electrons found in the phosphates can be rearranged in resonance fashion so that the triphosphate doesn’t fall apart automatically
when ATP is hydrolyzed, it yields energy
remember? nucleotide!
greater resonance stabilization as ADP and Pi
negative charges spread out
addition of phosphate to molecules increases the chemical potential energy
ATP and those “Other Compounds”
these phosphorylated compounds also have high free energies of hydrolysis:
- phosphoenolpyruvate (PEP): delta G = -61.9 kJ/mol
- 1,3 bisphosphoglycerate: delta G = - 49.3 kJ/mol
- phosphocreatine: delta G = -43.0 kJ/mol
Know these above compounds!
ATP and those “Other Compounds” - Thioesters
another class of intermediates that are also energy carriers:
thioesters!
hydrolysis of acetyl coenzyme A has a delta G of -31.4 kJ/mol
Energy Releasing Reaction? ATP
a key link between catabolism and anabolism
hydrolysis is very favorable (large, negative delta G
but the rxn is very slow and requiring enzymatic catalysis
not only is delta G large, but, taking into consideration the actual concentrations of recatants and products in cells, the delta G is even larger, typically -50 to -65 kJ/mol
the delta G varies from cell to cell depending on the concentrations
What is so special about ATP?
ATP is “mid” so it is in an intermediate position compared to the other molecules
- Using “high energy compounds” to carry out “low energy” reactions is a waste of energy.
- Using PEP (-70 kJ/mol) to help out a -20 kJ/mol reaction is a waste of 50 kJ/mol
- Whereas using ATP (~30-35 kJ/mol) would be a “waste” of 10-15 kJ/mol→efficient because it is wayyyyy less than the energy that PEP wastes
What is so special about ATP?
ATP is versatile
- It can transfer and receive phosphate groups and energy to and from high and low energy compounds
- ATP can undergo several different hydrolysis reactions, yielding different products and energies depending on need
- More than hydrolysis→group transfers
But also…
there are different ways to spilt (hydrolyze) ATP
a group is attached/transferred to some molecule
1 - to yield ADP + phosphoryl group
2 - to yield AMP + the pyrophosphoryl group (PO4PO3^3-
3- to yield pyrophosphate (PPi) + adenylyl group
- following this rxn, pyrophosphate can be hydrolyzed to yield 2 Pi (almost doubling the energy yield)
See, ATP is versatile!
different types of hydrolysis yield different amounts of energy
ATP to ADP + Pi delta G = -30.5 kJ/mol
ATP to adenylyl + PPi delta G = -45.6 kJ/mol
PPi to 2Pi delta G = -19.2 kJ/mol
note that ATP to adenylyl + PPi delta G = -45.6 kJ/mol which is the highest energy that has been yielded
ATP to adenylyl + PPi delta G = -45.6 kJ/mol
coupled with PPi to 2Pi delta G = -19.2 kJ/mol yields:
-45.6 - 19.2 = -64.8 kJ/mol
See, ATP is versatile! – Example
Big energy hill to climb!
- Adenylylation (transferring an
AMP) gives a lot of energy - AMP’ed up if you will…
- Fatty acid, amino acid activation,
DNA/RNA synthesis
Adenylyl is transferred to the fatty acid and PPi is released
Adenylyl is subsequently replaced by coenzyme A
Typically…and you’ll see this a lot – Phosphoryl Group Transfers
like with the glutamate to glutamine rxn
Phosphoryl Group Transfers
1- from ATP to various NDP’s
ATP + NDP (or dNDP) to ADP + NTP (or dNTP)
delta G = 0
2 - to reduce [ADP] when it becomes too high
2ADP to ATP + AMP
delta G = 0
- from creatine phosphate (phosphocreatine)
- a ready source of phosphoryl groups for quick synthesis of ATP (phosphocreatine is larger replenished by phosphoryl transfer from ATP)
ADP + PCr to ATP +Cr
delta G = - 12.5 kJ/mol
Oxidation/Reduction
One compound is oxidized. losing/releasing electron(s); another compound is reduced, gaining electron(s) [LEO says GER or OIL RIG]
sources of electrons:
- non-photosynthetic organisms: reduced compounds
- photosynthesis organisms: species excited by light
principle: the flow of electrons can do work (electromotive force, “emf”)
flow is from a relatively reduced compound to a relatively oxidized compound
this usually involves redox pairs
Fe^2+ to Fe3+ + e-
Cu^2+ + e- to Cu+
Fe2+ + Cu2+ to Fe3+ + Cu+
Oxidation/Reduction tips and things :)
MoreH’s→ more reduced
- MoreO’s→ more oxidized
*Oxidation → loss of electrons or time spent with electrons
Oxygens pull electron density away from carbon
highly oxidized means the most amount of oxygens
highly reduced is the most amount of hydrogens
types of electron transfer
1 - directly, as electrons (ex: metal ions)
2 - as hydrogen atoms (H+ + e-)
3 - as a hydride ion (H-)
4 - in combination with oxygen (from O2)
oxidation-reduction energetics
glucose (C6H12O6) + 6O2 to 6CO2 + 6H2O
delta G = -2840 kJ/mol
in a living system, this rxn takes place in many steps with electrons being removed at various steps
the electrons are transferred to coenzymes specialized for carrying electrons: NAD & FAD
metabolism diagram
glycolysis
glucose to pyruvate = 2 ATP (substrate level)
pyruvate to acetyl CoA then goes into mitochondria (substrate level)
electrons removed from acetyl CoA in the CAC = 2 ATP
electronc via NADH & FADH2 move to the oxidative phosphoylation electron transport and chemiosmosis = 34 ATP (oxidative level)
nicotinamide adenine dinucleotide (phos)
NAD(P)+
Mobile!/Loosely bound coenzyme
- Transfers electrons in pairs!
- Electron shuttle!
usually “free” in cells: an electron carrier
NADH (reduced)
NAD+ (oxidized)
dietary connection
NAD + NADP are derived from B viatmina niacin, which is in turn derived from typrtophan
but mosyt humans cannot synthesize enough, so we must have it in our diet (viatmin = required in small amounts
nacin defiicianec leads to low levels of NAD and NADP
one resultant disease is pellagra
you get this from:
- Vitamin B3
* Supplements
- Tuna, Peanuts, Salmon, Turkey, Chicken, Sunflower seeds, beef, pork
flavin nucleotides: FMN/FAD
usually bound (flavoprotein) stores electrons in cells
tightly bound to flavoproteins
holds electrons for the cells
is the redox bit. (cofactor) of the enzyme protein
dietary connection
FMN & FAD are derived from the b vitamin riboflavin
riboflavin deficiency leads to low levels of FMN & FAD
Get from
- vitamin B2
- Meat, yogurt, cheese, eggs, fortified grains, nuts, spinach
- Vegetarians and pregnant people at high risk of deficiency
For a given reaction, ∆H = -10.6 kJ/mol and ∆S = + 7.8 kJ/mol-K. This reaction is clearly…
A. Endothermic
B. Endergonic
C. Exergonic
D. None of the above
C. Exergonic
given these conditions, which of the following will happen initially:
fru 6-phos (1.5M) <-> Glu 6-phos (0.5M)
delta G = -4.4 kJ/mol
the rxn will proceed from left to right
the rxn will proceed from right to left
the system is at equilibrium
the rxn will proceed from left to right
because the delta G is negative and is spontaneous and there is reactants than products
given these conditions, which of the following will happen initially:
fru 6-phos (0.2M) <-> Glu 6-phos (1.8M)
delta G = +3.7 kJ/mol
the rxn will proceed from left to right
the rxn will proceed from right to left
the system is at equilibrium
the rxn will proceed from right to left
because the delta G is positive and there is more products than reactants
