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Flashcards in Energy Deck (41):
1

What is energy from a thermodynamic perspective?

- order

2

Gibbs energy

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

3

A reaction with a - delta G

increases disorder and is favored

4

A reaction with a + delta G

- creates order and is not favored
- do not take place spontaneously

5

For a reaction with a + Delta G to occur

- they must be coupled with a reaction with a high - Delta G
- couple formation of a peptide bond with GTP hydrolysis

6

Delta G measured in

calories

7

ATP

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

8

metabolism

- sum of anabolism and catabolism

9

anabolism

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

10

catabolism

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

11

reduction potential stored as

NADH

12

energy stored as

ATP

13

autotrophs

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

14

heterotrophs

- eat things from the environment that are already ordered

15

both

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

16

Making ATP

- substrate level phosphorylation
- oxidative phosphorylation

17

substrate level phosphorylation

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

18

Oxidative phosphorylation

- 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

19

Electron transport chain

- 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

20

Proton Motive Force

- 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

21

NADH, the driver

- 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

22

How NADH drives electron transport

- 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

23

The electron donor

- 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

24

redox potential

- how easily a compound can be oxidized or reduced
- measured in volts and expressed as Eo'

25

Redox span

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

26

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

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

27

Electron Transfer

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

28

The first two rely on

- 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.

29

Iron-Sulfur clusters

- 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

30

The S atoms are

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

31

Heme

- 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

32

Quinone

- hydrophobic hydrocarbons which reside in the membrane
- carry protons and electrons

33

Q cycle

- 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

34

Flavin

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

35

NADH Dehydrogenase

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

36

Ubiquinone/Ubiquinol

- 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

37

Cytochrome bc1

- 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

38

Cytochrome c

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

39

Cytochrome c oxidase

- e- passed to a heme (mV=290) to O2 to form H2O mv=816
- 1 H+ pumped/electron

40

ETC and ATP synthesis

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

41

The F0F1 ATPase

- 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