Lectures 3 &4: Bioenergetics and Metabolism

Question 1

Heterotropic regulation

Answer 1

s

Question 2

Homotrophic regulation

Answer 2

w

Question 3

Autotroph

Answer 3

e

Question 4

Heterotroph

Answer 4

e

Question 5

Gibbs free energy

Answer 5

The capacity to do work at a constant temperature and pressure

Question 6

enthalpy, delta H

Answer 6

heat

Question 7

Entropy, delta s

Answer 7

• The amount of disorder in a system
• While entropy of a SYSTEM can decrease in a given reaction, entropy of the UNIVERSE always either increases or remains constant
• Can be increased by simply increasing number of molecules or increasing number of molecules in a more “entropic” state, which decreases order and “information (ex: 7 solid molecules to 7 gaseous molecules, or 26 letters of the alphabet all lined up in alphabetical order vs in a mishmash)

Question 8

∆G°’

Answer 8

-Free energy of a reaction under standard biological conditions, meaning
- 1 atm
- 25 degrees celsius
- pH of 7
- 1 molar concentration of everything EXCEPT hydrogen ions, b/c that would be too low of a pH for biological function
=-RTlnKeq
- Equation above tells you how far to the left or the right a reaction will go under standard conditions

Question 9

∆G°

Answer 9

-Free energy under standard conditions

Question 10

Keq

Answer 10

Equilibrium Constant
If Keq is less than one, the reaction is not spontaneous b/c we have more reactants than products at equilibrium
If Keq is greater than one, the reaction is spontaneous b/c we have more products than reactants at equilibrium (for our purposes)
- Can be predicted by ∆G°’ (even though technically i think ∆G°’ calculated by Keq); VERY SMALL CHANGES IN ∆G°’ GIVE LARGE CHANGES IN Keq

Question 11

spontaneous

Answer 11

-Occurs forward on its own without being driven by some outside force; does NOT mean it occurs quickly, however

Question 12

ATP

Answer 12

• Adenosine triphosphate
• It contains a lot of energy b/c it has three highly negative phosphate groups next to each other, and removing one releases a lot of energy, and also because when a free phosphate group is in aqueous solution, it has more resonance forms available to it then when in ATP
• Even though the reaction from ATP–> ADP has a very negative ΔG, it has a very high activation energy, which is why ATP doesn’t just convert to ADP quickly. It DOES convert spontaneously (because of the negative delta G), just kinetically very slowly
• ATP hydrolysis happens in the cytosol

Question 13

AMP

Answer 13

-Adenosine monophosphate

Question 14

leaving group

Answer 14

d

Question 15

committed step

Answer 15

• A step that has a very large, negative ΔG, so it is difficult to go backwards b/c the activation energy is SO LARGE now
• Once the reaction has gone past this step, there’s essentially no going back
• There can be multiple committed steps in a pathway
• Committed steps are typically the steps that are regulated by enzymes and whatnot in a pathway

Question 16

rate-limiting step

Answer 16

-The step that has the highest activation energy and goes the slowest. Since it goes the slowest, the rate of the reaction is confined to this step, no matter how fast the other steps are, hence why it is rate-limiting.

Question 17

flux

Answer 17

r

Question 18

redox reaction

Answer 18

• Reduction/Oxidation reaction
• Can’t have one without the other, although you can separate the two in space (think the salt bridges and galvanic cell potentials from chemistry)
• Biology typically oxidizes things by removing a hydride and reduces things by adding a hydride

Question 19

half-cell reaction

Answer 19

• Half of a redox reaction; either the reduction or the oxidation

Question 20

E, 1/2 cell potential

Answer 20

• The reduction potential
• The higher the E, the more something wants to be reduced, the lower the E (the more negative it is), the more it want to be oxidized
• The E of the reduction and oxidation reactions being done are added together, but it is important to know that since the E is the REDUCTION potential, in order to get the OXIDATION potential, you need to add a negative sign

Question 21

e donor

Answer 21

e

Question 22

e acceptor

Answer 22

e

Question 23

NAD/NADH

Answer 23

• NADH is an electron carrier, carrying elections in the form of a hydride (H-)
• NAD + is the OXIDIZED form and NADH is the REDUCED form since it now has a hydride attached
• Carriers don’t LOVE being reduced, and they don’t LOVE being oxidized, which makes them good carriers b/c they can relatively easily gain and give up hydrides
• Transfer electrons as a pair (2) since hydride has two electrons

Question 24

NADP/NADPH

Answer 24

• Exact same structure as NAD/NADH, except has a phosphate attached at C2 carbon of one of the riboses
• Has the same “business end” as NAD/NADH
• Since it has that extra phosphate, some enzymes prefer it, while other enzymes prefer NAD
• NADPH is almost always a reducing agent, and NAD+ is almost always used as an oxidizing agent

Question 25

niacin

Answer 25

- Niacin is a vitamin - The reduced form of the "business end" of NADP is a moiety of niacin - moiety: one of two or more parts into which something may be divided, such as various parts of a vitamin or molecule

Question 26

FMN

Answer 26

- An electron carrier that transfers electrons as hydrogen radicals, which is a hydronium ion and a single electron - Transfers electrons one at a time

Question 27

FAD

Answer 27

An electron carrier that transfers electrons as hydrogen radicals, which is a hydronium ion and a single electron - Transfers electrons one at a time

Question 28

riboflavin

Answer 28

- A vitamin that contains a moiety that is the "business end" of FAD and FMN

Question 29

Glycolysis

Answer 29

- The production of ATP from ADP, done by coupling this reaction with the oxidation of glucose. The whole reason this is able to occur is because the breakdown of glucose gives off more energy than it takes to form ATP( this might be glycolysis + Krebs, not sure though) - Basically, glycolysis forms molecules with inorganic phosphates attached to them that are even more prone to releasing the phosphates than ATP is so they release more energy in doing so, allowing the Pi group to get transferred directly to ADP - First step in the breakdown of glucose - Uses two ATP to phosphorylate the sugar on the 1 and 6 carbons - Has a net production of 2 ATP - Can happen in the absence of O2; does NOT use oxygen - Happens in the cytosol

Question 30

∆G

Answer 30

Free energy of "unstandard" condition; distribution of products to reactants under some different circumstances. If asking for ∆G, we are NOT under equilibrium conditions

Question 31

kinase

Answer 31

An enzyme that phosphorylates things

Question 32

phosphatase

Answer 32

An enzyme that removes a phosphate group from molecules

Question 33

exergonic reaction

Answer 33

- A reaction that produces a lot of energy | - The hydrolysis of ATP is exergonic