biochem & nutrition exam 1

Question 1

1st and 2nd law of thermodynamics

Answer 1

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

Question 2

What makes a reaction go? Energetics/Thermodynamics

Answer 2

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)

Question 3

Energetics/Thermodynamics
entropy (S)

Answer 3

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

Question 4

Energetics/Thermodynamics
Gibbs Free Energy (G) is the available energy in a system to do work.

Answer 4

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

Question 5

exergonic vs endergonic

Answer 5

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)

Question 6

delta G = delta H - TdeltaS

Answer 6

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])

Question 7

equilibrium

Answer 7

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

Question 8

Keq

Answer 8

= 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

Question 9

will a rxn occur under actual conditions? the answer depends on delta G, not just delta G knot

Answer 9

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

Question 10

IF: Keq > 1, ∆G° is large and negative→meaning?

IF: Keq < 1, ∆G° is large and positive→meaning?

Answer 10

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

Question 11

thermodynamics of biosystems

Answer 11

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)

Question 12

catabolism & anabolism

Answer 12

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

Question 13

catabolism & anabolism

Answer 13

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

Question 14

Reaction Coupling

Answer 14

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.

Question 15

more thermodynamics

Answer 15

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

Question 16

Reaction Coupling

Answer 16

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.

Question 17

Energy Releasing Reaction? ATP and other compounds!

Answer 17

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)

Question 18

Energy Releasing Reaction? ATP and other compounds!

Answer 18

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

Question 19

ATP and those “Other Compounds”

Answer 19

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!

Question 20

ATP and those “Other Compounds” - Thioesters

Answer 20

another class of intermediates that are also energy carriers:
thioesters!

hydrolysis of acetyl coenzyme A has a delta G of -31.4 kJ/mol

Question 21

Energy Releasing Reaction? ATP

Answer 21

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

Question 22

What is so special about ATP?

Answer 22

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

Question 23

What is so special about ATP?

Answer 23

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

Question 24

But also…
there are different ways to spilt (hydrolyze) ATP

Answer 24

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)

Question 25

See, ATP is versatile!

Answer 25

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

Question 26

See, ATP is versatile! – Example

Answer 26

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

Question 27

Typically…and you’ll see this a lot – Phosphoryl Group Transfers

Answer 27

like with the glutamate to glutamine rxn

Question 28

Phosphoryl Group Transfers

Answer 28

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

3. 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

Question 29

Oxidation/Reduction

Answer 29

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+

Question 30

Oxidation/Reduction tips and things :)

Answer 30

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

Question 31

types of electron transfer

Answer 31

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)

Question 32

oxidation-reduction energetics

Answer 32

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

Question 33

metabolism diagram

Answer 33

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)

Question 34

nicotinamide adenine dinucleotide (phos)
NAD(P)+

Answer 34

Mobile!/Loosely bound coenzyme

• Transfers electrons in pairs!
• Electron shuttle!

usually “free” in cells: an electron carrier

NADH (reduced)
NAD+ (oxidized)

Question 35

dietary connection

Answer 35

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

Question 36

flavin nucleotides: FMN/FAD

Answer 36

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

Question 37

dietary connection

Answer 37

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

Question 38

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

Answer 38

C. Exergonic

Question 39

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

Answer 39

the rxn will proceed from left to right
because the delta G is negative and is spontaneous and there is reactants than products

Question 40

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

Answer 40

the rxn will proceed from right to left
because the delta G is positive and there is more products than reactants