Lecture 8: Intro to Metabolism

Question 1

Define Catabolism

Answer 1

breaking down compounds to be stored as a high-energy intermediate

Question 2

Define anabolism

Answer 2

the synthesis of macromolecules using simple building blocks and energy

Question 3

Define metabolism

Answer 3

the catabolism of compunds releasing free energy that can be stored as ATP or other high-energy intermmediates such as NADH, NADPH, and FADH2

Question 4

Describe the effect of Gibbs free energy on metabolism

Answer 4

influences metabolic flux and/or the conversion of metabolites through pathways since it determines how much energy is available for bond formation

Question 5

Describe the equation for gibbs free energy change

Answer 5

gibbs free energy change= standard free energy change + rate law constant x Time x natural logarithm of the concentration of products over sunstrates

Question 6

What are the conditions for standard free energy change in biochemistry

Answer 6

1M [H+], 298K, pH 7

Question 7

Describe the equation for standard free energy change

Answer 7

standard free energy change= negative rate law constant x temperature x natural logarithm x equillibrium constant

Question 8

What does Keq represent

Answer 8

Equillibrium constant, or the concentration of products over substrates at equillibrium

Question 9

What is standard free energy change when the equillibrium constant is greater than one

Answer 9

negative

reaction is exergonic (spontaneous)

will have more product

Question 10

What is standard free energy change when the equillibrium constant is less than one

Answer 10

positive

reaction is endergonic (nonspontaneous/unfavorable as written)

will have more substrate

the concentrations of substrates and products can influence directionality and overcome an unfavorable standard free energy change

Question 11

What is standard free energy change when the equillibrium constant is equal to one

Answer 11

zero

reaction is reversible

equal amounts of substrate and products

Question 12

What is the standard gibbs free energy dependant upon

Answer 12

the nature of the reactants and their concentrations at equillibrium (Keq value)

Question 13

What is the cellular gibbs free energy dependant on

Answer 13

the cellular concentrations of substrate and product

Question 14

How can enzymes speed up a reaction

Answer 14

speed up a reaction by creating an active site that binds to substrates and lowers the activation energy (creates a transition state). They can couple an unfavourable reaction with a favourable one in order to create a new reaction that is favourable

Question 15

Why must catabolic and anabolic pathways be regulated in a cell?

Answer 15

• anabolic pathways may require high energy
• both pathways utilize similar substrates and products; some substrates for anabolism are products from catabolism, so if noth happen at the same time you will not have sufficient ressources for either reaction

Question 16

Why there is more energy in the hydrolysis of ATP to AMP and PPi versus the hydrolysis of ATP to ADP

Answer 16

The hydrolysis of different phosphohydride bonds (alpha v gamma) have different free energies due to the stability of their products

PPi is unstable because of its negative charges and AMP is ressonance stabalized, meaning that PPi is rapidly hydrolyzed to 2Pi, releasing more energy

Pi is ressonance stabalized but ADP is still unstable, meaning less energy is released

Question 17

How can ATP hydrolysis be changed to produce AMP and PPi versus ADP

Answer 17

cleavage of alpha bond = AMP + PPi
cleavage of gamma bond = ADP +Pi

Question 18

What is ATP composed of

Answer 18

adenine, ribose, and three phosphates (alpha, beta, gamma) linked by ohosphoanhydride bonds and an ester bond to the sugar

Question 19

Why are free energy changes not fixed

Answer 19

The polar phosphates are ionizable and pH dependant

metal ions (cofactors) help with stabalization

Question 20

What metal ion is a common cofactor for ATP stabilization

Answer 20

Mg2+

Question 21

What effect will a pH decrease have on the amount of free energy released

Answer 21

Will result in a decrease in free energy release

More protons available results in less repulsion between negative charges, creating a stabilized reactant

Question 22

What effect will the presence of Mg2+ have on the amount of free energy released

Answer 22

Will result in a decrease in free energy release

Will bind negative charges, causing both substrates AND products to be stabilized and lower in energy

Reactants will be more effected

Question 23

What is nucleoside diphosphokinase

Answer 23

enzyme that facilitates the transfer of a phosphate from ATP to ADP to form ATP and GDP and vice versa

Question 24

What is phosphoryl transfer potential

Answer 24

ATP carries phosphoryl groups, which allows it to drive reactions that require an imput of free energy

Question 25

What molecule has the most negative standard free energy change of hydrolysis? Why?

Answer 25

phosphoenolpyruvate very unstable structure

Question 26

How can you determine if a molecule can be used to make ATP

Answer 26

if it has a more negative standard free energy change of hydrolysis than -32kJ/mol (ATP to ADP and Pi)

Question 27

What does creatine kinase do

Answer 27

Catalyzes a coupled reaction as a transferase that transfers the phosphte from phosphocreatinine to ADP in an exercising cell to produce ATP and creatine Controlled by gibbs free energy changes

Question 28

How can creatine be obtained in a cell

Answer 28

can be synthesized from amino acids or taken as a supplement

Question 29

What is the standard free energy change for the phosphate transfer reaction catalyzed by creatine kinase to regenerate ATP

Answer 29

-12kJ/mol (under standard conditions

Question 30

Describe the role and free energy of phosphocreatine

Answer 30

A storage form of phosphates that can be used to make ATP in muscle Has a larger, negative standard free energy change compared to ATP (therefore can be used to make ATP)

Question 31

How can the ADP+phosphocreatine to ATP+ creatine reaction be reversed

Answer 31

By adjusting the concentration of products to generate a new, positive standard free energy change

Question 32

What are five ways a reaction pathway can be regulated

Answer 32

1) concentration of metabolites 2) availability of enzymes (synthesis/degradation) 3) inhibition of enzymes 4)function of enzyme

Question 33

What are two ways enzyme availability can be regulated

Answer 33

Regulation of synthesis through transcriptional and translational regulation Regulation of degradation through denaturation (heat, pH) and breakdown (protease activity)

Question 34

How can the function of an enzyme be regulated

Answer 34

availability of cofactors, post-translational modifications (acetylations, phosphorylations), mutations