Bioenergetics And Thermodynamics

Question 1

how do u calculate change in free energy?

Answer 1

Question 2

what determines the speed of a rxn?

Answer 2

activation energy

Question 3

what does G tell us about the rate of the reaction?

Answer 3

NOTHING

Question 4

why might adding heat to a rxn to speed it up not be smart?

Answer 4

it is non-specific

Question 5

what is [s/p], pH, T and pressure at chemical standard conditions?

Answer 5

[ ] = 1M
PH = 0
T = 25 degrees C or 298 K
Pressure = 1atm

Question 6

what does Keq and ΔG° measure?

Answer 6

the tendency for a rxn to proceed spontaneously

Question 7

how do u calculate change in free energy of a rxn at eq?

Answer 7

Question 8

where is a reaction proceeding from to?

Answer 8

from standard conditions to eq

Question 9

what is [s/p], pH, T , [H2O] and [Mg2+] for biochemical standard conditions?

Answer 9

[s/p] = 1M
pH = 7
T = 25 degrees C or 298 K
[H2O] = 55.5M
Mg2+ = 1mM

Question 10

if Keq > 1 what does this tell us abt the rxn?

Answer 10

(-) ΔG° = rxn will proceed forwards

Question 11

if Keq < 1 what does this tell us abt the rxn ?

Answer 11

(+) ΔG° =rxn will proceed in the reverse

Question 12

if Keq = 0 what does this tell us abt the rxn?

Answer 12

the rxn is at equilibrium ΔG° = 0

Question 13

why is the Keq not used to determine actual free energy change?

Answer 13

becaused actual free energy change is rarely at equilibrium

Question 14

what is the equation to determine actual free energy change

Answer 14

Question 15

what does the actual free energy of a reaction depend on?

Answer 15

the [P] and [R]

Question 16

what do we need to know in order to determine delta G’ at non-Eq conditions?

Answer 16

[ ] or ratios of P/R

Question 17

what units must delta G’, R and T be in to use nernst equation?

Answer 17

Delta G’ = J/mol
R = J/mol -K
T = Kelvin

Question 18

when can delta G’ at standard conditions be determined?

Answer 18

if you know [P/R] at equilibrium

Question 19

what is needed for the energy released by an exergonic process to drive an endergonic process - and vice versa?

Answer 19

a common intermediate

Question 20

what is the difference between direct and indirect coupling?

Answer 20

direct coupling uses the same enzyme to drive both reactions while indirect coupling uses 2 different enzymes

Question 21

what is the delta G’ for the conversion of glucose to G6P (phosphorylation of glucose)?

Answer 21

~ -17 kj /mol

Question 22

what is the delta G for the hydrolysis of ATP?

Answer 22

~ -30kj/mol

Question 23

what is a common product of endergonic reactions that is also a common intermediate?

Answer 23

Pyrophosphate (PPi)

Question 24

how much energy is released when breaking phosphoester bonds?

Answer 24

-16kj / molho

Question 25

what makes ATP a metastable compound?

Answer 25

kinetically stable - high activation energy thermodynamically unstable - high amount of energy released

Question 26

what makes Mg2+ so important in metabolism?

Answer 26

Mg2+ and ATP have to bind together as a substrate -Mg++ activates ATP

Question 27

why is delta G for ATP hydrolysis only an estimate?

Answer 27

because it depends on [Mg++]

Question 28

what is the difference between a phosphate transfer and phosphorylation?

Answer 28

A phosphate transfer does not use Pi

Question 29

what makes substrate level phosphorylation important in metabolism?

Answer 29

O2 is not needed and it always generates an NTP - ATP can be made without oxygen

Question 30

how much energy is released from the hydrolysis of phosphocreatine? what makes this so high?

Answer 30

-43kj / mol - more than ATP due to it being a phosphagen (phosphoamide with a higher group transfer potential than ATP

Question 30

what does phosphocreatine react with to make ATP? what is the by-product?

Answer 30

Phosphocreatine + ADP + H+ ---------> Creatine + ATP

Question 31

what is the importance of creatine?

Answer 31

it boosts power output in anaerobic conditions -repetitive high intensity

Question 32

How much energy is released from the hydrolysis of acetylCoA (thioester)? what are the bi-products

Answer 32

-31 kj / mol -CoA-SH (co enzyme A) and a carboxylic acid

Question 33

how is an acyl group produced?

Answer 33

the removal of OH from an oxoacid (usually carboxylic acid)

Question 34

how is coenzyme A activated

Answer 34

attachment of acetate or an acyl group to form acyl CoA or Acetyl CoA

Question 35

what 3 way can the body generate ATP?

Answer 35

1) oxidative phosphorylation - phosphorylation of ADP to ATP coupled to ETC 2) Substrate-level phosphorylation- direct transfer of phosphate group 3) ADK reaction ( adenylate kinase) synthesizes ATP from 2 ADP

Question 36

what is the Adenylate Kinase reaction?

Answer 36

ADP + ADP --> ATP + AMP

Question 37

what are the products of adenylate kinase reaction?

Answer 37

AMP and ATP

Question 38

why is the production of AMP from the adenylate kinase reaction so important?

Answer 38

AMP activates AMP dependent kinase which turns ON catabolic pathways and OFF anabolic pathways

Question 39

what stimulates increases in AMP kinase?

Answer 39

changes in the ATP-to-AMP ratio, AMPK is activated and phosphorylates downstream targets to redirect metabolism towards increased catabolism and decreased anabolism

Question 40

how does AMP affect PFK-1?

Answer 40

AMP stimulates PFK-1, enhancing glycolysis and energy production when cellular energy is low

Question 41

how is the adenylate kinase reaction useful other than production of ATP from ADP?

Answer 41

Drives the reverse rxn to be able to convert AMP to ATP

Question 42

what is transphosphorylation? where is this specifically important?

Answer 42

the transfer of a phosphate from one nucleotide to another -important in G proteins to convert GDP to GTP

Question 43

what enzyme is used in transphosphorylation?

Answer 43

Nucleoside diphosphate Kinase (NDK)

Question 44

how is the transfer of nucleotides in transphosphorylation achieved?

Answer 44

phosphate is added to the enzyme and then removed from the enzyme to a NDP -ping pong rxn

Question 45

what enzyme would be used to catalyze this transphosphorylation?

Answer 45

ADK or Myokinase

Question 46

what is adenylate kinase also known as?

Answer 46

Myokinase

Question 47

What are the 3 stages of aerobic catabolism?

Answer 47

1) breakdown of C backbone to generate Acetyl-CoA and NADH/FADH 2) Citric Acid Cycle - breakdown of acetyl-CoA 3) Oxidative phosphorylation

Question 48

where should the electrons belong to when considering oxidation state?

Answer 48

the most EN atom

Question 49

what is the equation used to determine oxidation state of a carbon atom?

Answer 49

of valence (4) - # of lone pair electrons + assigned electrons

Question 50

what are assigned electrons and what does this largely depend on?

Answer 50

he electrons that are counted as belonging to an atom in a compound or ion - depends on EN of the atom attached to Carbon

Question 51

what 4 ways can electrons be transferred?

Answer 51

1) as electrons 2) as hydrogen atoms 3) as hydride ion 4) direct combination with oxygen

Question 52

what are oxidoreductases?

Answer 52

Oxidoreductases are a class of enzymes that facilitate oxidation-reduction (redox) reactions, which involve the transfer of electrons between molecules

Question 53

what is oxygenase? how is it classified?

Answer 53

enzyme that oxidizes a substrate by transferring O2 to it -mono-oxygenase, dioxygenase...etc (transfer of 1 or more O2)

Question 54

what is an oxidase?

Answer 54

an enzyme that catalyzes an Ox-red rxn involving O2 as an electron acceptor

Question 55

what is a dehydrogenase?

Answer 55

An enzyme that removes hydrogen + electrons

Question 56

what is the flow of electrons based on in redox rxns?

Answer 56

the affinity of a molecule for electrons

Question 57

what is oxidation typically synonymous with?

Answer 57

dehydrogenation

Question 58

what does NAD+ being a cosubstrate tell us about it's binding?

Answer 58

it binds loosely

Question 59

what does FAD as a prosthetic group tell us about its binding

Answer 59

it binds tightly

Question 60

what absorbance peak can you expect to see NAD+ at?

Answer 60

1 peak ~260nm

Question 61

what absorbance peak can you expect to see NADH at?

Answer 61

2 peaks, one around 260nm and another around 340nm

Question 62

what enzyme converts lactate to pyruvate? what else does this rxn produce?

Answer 62

LDH -converts NAD+ to NADH

Question 63

what does it mean if LDH is seen in blood?

Answer 63

NADH will appear and this can mean serious health issues such as heart attack

Question 64

what is the arbitrary standard of reduction potential?

Answer 64

the half reaction of hydrogen 2H+ +2e- <--> H2 0 volts at standard conditions

Question 65

what is the reduction potential of hydrogen at pH 7?

Answer 65

-0.421V

Question 66

what is the reduction potential of hydrogen at standard conditions?

Answer 66

0 volts