Biochemistry Ii

Front 1

What does one call the reaction when the free energy and equilibrium constants are close to zero?

Back 1

near-equilibrium reaction

Front 2

Where do most enzymes in a metabolic pathway act?

Back 2

At equilibrium

Front 3

Which reactions, when considering enzymes, are irreversible?

Back 3

exergonic rxns

Front 4

Living organisms are thermodynamically open or closed living systems?

Back 4

open

Front 5

What sets the flux rate in a pathway?

Back 5

rate-determining step

Front 6

What are two major qualities of the rate-determining step?

Back 6

1. functions far from equilibrium
2. has a large negative free energy change

Front 7

Phosphorylated

Back 7

attatchment of a phosphoryl group

Front 8

Substrate cyle

Back 8

two opposing metabolic reactions that function together to hydrolyze ATP, but provide a control point for regulating metabolic flux

Front 9

Can an equilibrium process perform useful work? (G=0)

Back 9

no

Front 10

What do reactions that function near equilibrium respond rapidly to?

Back 10

Changes in substrate concentration

Front 11

What do a series of near-equilibrium reactions downstream from the rate-determining step have in common?

Back 11

same flux

Front 12

Allosteric control

Back 12

enzymes controlled by effectors that can be substrates, products or coenzymes of the pathway

Front 13

Name four ways cells control metabolic flux.

Back 13

CAGS
-Allosteric control
-Covalent Modification
-Substrate cycles
-Genetic control

Front 14

What type of acid is palmitate?

Back 14

fatty acid

Front 15

Why does oxidative metabolism proceed in a stepwise fashion?

Back 15

So the released free energy can be recovered in a manageable form at each exergonic step

Front 16

"high energy intermediates"

Back 16

packets of energy that undergo exergonic breakdown to drive endergonic processes

Front 17

What are some forms of energy currency that the cell uses?

Back 17

-phosphorylated compounds like nucleotide ATP
-compounds containing thioester bonds
-reduced coenzymes like NADH

Front 18

Does ATP occur in all lifeforms?

Back 18

yes

Front 19

From what does ATP get its biological importance?

Back 19

the large free energy change that accompanies cleavage of its phosphoanhydride bonds

Front 20

What are the two things that can be transferred when these bonds break?

Back 20

-phosphoryl group transferred leaving behind ADP
-nucleotidyl (AMP) group is transferred leaving pyrophosphate

Front 21

Phosphoryl group-transfer potentials

Back 21

measure of the tendency of phosphorylated compounds to transfer their phosphoryl groups to water

Front 22

Does a favorable free energy change indicate how fast the rxn occurs?

Back 22

no

Front 23

Are ATP and other phosphorylated compounds kinetically stable?

Back 23

yes

Front 24

How large does the negative value for free energy have to be for something to be considered high energy?

Back 24

greater than -25 kJ/mol

Front 25

Bond energy

Back 25

energy required to break a covalent bond

Front 26

What factors are responsible for the "high energy" character of phosphoanhydride bonds like those in ATP?

Back 26

-resonance stabilization of a phosphoanhydride bond is less than that of its hydrolysis products
- (most important) destabilization effect of the electrostatic repulsions between the charged groups of a phosphoanhydride compared to those of its hydrolysis products
-phosphoanhydride has a smaller solvation energy when compared to those of its hydrolysis products

Front 27

What is the initial step in the metabolism of glucose?

Back 27

conversion to glucose-6-phosphate

Front 28

Hexokinase catalyzes theh formation of what?

Back 28

glucose-6-phosphate (catalyzes the transfer of a phosphoryl group from ATP directly to glucose)

Front 29

ATP hydrolysis

Back 29

phosphoryl group transfer is directly to water

Front 30

What does it mean when one says ATP hydrolysis is thermodynamically favored but kinetically disfavored? (explain example from book)

Back 30

the reaction of glucose with ATP that yields glucose-6-phosphate: the activation energy for the nonenzymatic transfer of a phosphoryl group from ATP to glucose is greater than that for ATP hydrolysis, so without hexokinase, the hydrolysis reaciton predominates

Front 31

ATP breaking down to ADP and Pi

Back 31

orthophosphate cleavage

Front 32

ATP breaking down to AMP and PPi

Back 32

phyrophosphate cleavage

Front 33

Inorganic pyrophosphatase

Back 33

cleaves PPi into 2Pi

Front 34

What drives the pyrophosphate cleavage in the synthesis of an aminoacyl-tRNA to completion?

Back 34

irreversible hydrolysis of PPi

Front 35

Through what does ATP drive endergonic reactions?

Back 35

through exergonic process of phosphoryl group transfer and phosphoanhydride hydrolysis

Front 36

What is one way ATP can be regenerated?

Back 36

by coupling its formation to a more highly exergonic metabolic process

Front 37

Substrate-level phosphorylation

Back 37

ATP can be formed from ADP by direct transfer of a phosphoryl group from a "high-energy" compound

Front 38

Oxidative phosphorylation

Back 38

when ATP is generated indirectly using the energy supplied by transmembrane proton concentration gradients
(in oxidative metabolism)

- called photophosphorylation in photosyntheseis

Front 39

Kinases

Back 39

catalyze the flow of energy from "high-energy" phosphate compounds to ATP and from ATP to "low-energy" phosphate compounds

(the kinases actually transfer the phosphoryl groups