Energy

Question 1

What is energy from a thermodynamic perspective?

Answer 1

• order

Question 2

Gibbs energy

Answer 2

• the energy associated with a chemical reaction that can be used to do work

Question 3

A reaction with a - delta G

Answer 3

increases disorder and is favored

Question 4

A reaction with a + delta G

Answer 4

• creates order and is not favored

- do not take place spontaneously

Question 5

For a reaction with a + Delta G to occur

Answer 5

• they must be coupled with a reaction with a high - Delta G

- couple formation of a peptide bond with GTP hydrolysis

Question 6

Delta G measured in

Answer 6

calories

Question 7

ATP

Answer 7

• very ordered structure

- hydrolysis to ADP (between 2nd and 3rd phosphate bonds) have a negative delta G (releases ~11 kCal or energy)

Question 8

metabolism

Answer 8

• sum of anabolism and catabolism

Question 9

anabolism

Answer 9

• building of molecules
• requires energy
• reductive process
• coupled to ATP hydrolysis

Question 10

catabolism

Answer 10

• break down of molecules
• release energy
• oxidative process
• linked to formation of ATP

Question 11

reduction potential stored as

Answer 11

NADH

Question 12

energy stored as

Answer 12

ATP

Question 13

autotrophs

Answer 13

• use the energy from the sun (or reduced chemicals) to put order into CO2

Question 14

heterotrophs

Answer 14

• eat things from the environment that are already ordered

Question 15

both

Answer 15

• energy in the ordered molecules is released slowly and the stored energy is stored in a form the cell can use later.

Question 16

Making ATP

Answer 16

• substrate level phosphorylation

- oxidative phosphorylation

Question 17

substrate level phosphorylation

Answer 17

• a high energy compound can transfer its phosphate directly to ADP
• important when cells are grown anaerobically

Question 18

Oxidative phosphorylation

Answer 18

• energy is used to set up a proton gradient across a membrane which is used to drive an ATP synthase, combining ADP with inorganic phosphate.
• complete oxidation of the substrates all the way to CO2
• more efficient

Question 19

Electron transport chain

Answer 19

• driven by oxidation of reduced compounds,
• the energy released from the oxidation of these compounds is coupled to the transport of protons across the membrane
• energy extracted from reduced compounds is done in a stepwise fashion
• small packets of energy are released at discrete times so that each can be efficiently captured

Question 20

Proton Motive Force

Answer 20

• if the concentration of protons on one side of the membrane is larger than on the other, the protons on the more concentrated side will want to pass over to the other side
• chemical gradient and electrical potential = sum of these two forces

Question 21

NADH, the driver

Answer 21

• the normal electron acceptor
• one of the main ways the cell captures and stores reduction potential
• when an electron is extracted it can be passed to the oxidized form NAD+
• reduction potential stored in the form of NADH

Question 22

How NADH drives electron transport

Answer 22

• NADH dehydrogenase oxidizes NADH, withdrawing the electrons
• as electrons move through the complex, protons are pumped to the outside of the cell (this requires energy)
• electrons emerge from the complex at a LOWER REDOX potential, but with energy left
• electrons flow through other complexes, pump protons, until they reduce O2 to water

Question 23

The electron donor

Answer 23

• is more reduced than the electron acceptor
• more reduced = more energy = more willing to give electron
• the lower the number, the more reduced the compounds is

Question 24

redox potential

Answer 24

• how easily a compound can be oxidized or reduced

- measured in volts and expressed as Eo’

Question 25

Redox span

Answer 25

• Delta E
• Eo’ acceptor - Eo’ donor
• bigger redox span = more energy

Question 26

Why isn’t there an enzyme that can transfer the electron directly from NADH to O2?

Answer 26

• you would have a more difficult time extracting energy that way
• the electron loses just enough energy at each step to pump one proton

Question 27

Electron Transfer

Answer 27

• iron-sulfur clusters in proteins
• iron bound in heme
• the organic quinones
• organic flavin molecules

Question 28

The first two rely on

Answer 28

• Fe can very easily accept and donate electrons by going from the ferrous to ferric form
• they can also just transfer one electron
• organic carriers must transfer a proton to balance the charge.

Question 29

Iron-Sulfur clusters

Answer 29

• 2Fe-2s, 3Fe-4S, 4Fe-4S
• inserted into many redox proteins
• held in place by sulfur group of cysteine (S is not part of the cluster)
• electrons jump from Fe/S clusters

Question 30

The S atoms are

Answer 30

• acid labile

- treatment of the protein with acid would destroy the cluster and liberate the atoms

Question 31

Heme

Answer 31

• contain iron within a protoporphyrin ring structure
• Fe is the electron donor and acceptor
• ring structure has a different structure depending on type of heme - will change redox potential
• can be inserted into proteins covalently (in C-type cytochromes) or ionically
• heme-containing proteins are called cytochromes

Question 32

Quinone

Answer 32

• hydrophobic hydrocarbons which reside in the membrane

- carry protons and electrons

Question 33

Q cycle

Answer 33

• the quinone “pool” is found within the membrane and accepts electrons from a quinone binding site on complex I (NADH dehydrogenase)
• a proton is then picked up from the interior of the cell to balance the charge
• after picking up 1 electron and 1 proton, the molecule is a semiquinone
• after picking up 2 of each, it is a quinoa
• the hydrogen atoms picked up in the interior are dropped off outside the cell when the quinol gets oxidized by the next component of the chain
• not a proton pump but strengthens the PMF

Question 34

Flavin

Answer 34

• lacks hydrophobic tail
• FMN - isolated - found in proteins (complex I)
• FADH - bound to adenine nucleotide - soluble electron carrier
• carry both H+ and e-

Question 35

NADH Dehydrogenase

Answer 35

• 2 e- released
• redox potential of -320 mv
• electrons move through several iron clusters and a flavoprotein
• 2 protons pumped

Question 36

Ubiquinone/Ubiquinol

Answer 36

• 2e- bind to Ubiquinone (2H+ from the inside) form ubiquinol
• e- are donated to cytochrome bc1, protons are deposited on the outside
• 2 protons translocated
• e- now at 45 mV

Question 37

Cytochrome bc1

Answer 37

• e- are passed through 2 heme b, then to a heme c
• e- donated a soluble cytochrome C
• e- come in at 45 mV, leave at 254 mv

Question 38

Cytochrome c

Answer 38

• electrons passed from cytochrome c to the cytochrome c oxidase
• e- enter and leave at 254 mV

Question 39

Cytochrome c oxidase

Answer 39

• e- passed to a heme (mV=290) to O2 to form H2O mv=816

- 1 H+ pumped/electron

Question 40

ETC and ATP synthesis

Answer 40

• not strictly coupled
• all H+ pumped do not get used for oxidative phosphorylation
• used in flagella motor and active transporters

Question 41

The F0F1 ATPase

Answer 41

• F0 is the integral membrane motor portion
• F1 is soluble ATP producing portion
• F0 spins when the protons flow back into the cell along the gradient
• spinning motor attached to a gamma subunit that spins inside the soluble F1, transferring the power
• Nucleotide binding site (3 in F1)
• At any one time, one of the nucleotide binding sites will be empty, one will contain ADP+Pi, and the third will contain ATP
• gamma subunit spin, changing the conformation of the nucleotide binding site as it passes
• allows for access of ADP+Pi, catalyzes ADP+Pi->ATP reaction, or releases ATP