Bio Chap 14

More C-H bonds = reduction or oxidation?

reduction

• methane or CH4

Fewer C-H bonds = reduction or oxidation?

oxidation

• CO2 or carbon dioxide

counting C-H bonds tracks oxidation state photo

reduction

• accompanied by hydrogenation (adding H+)

• A + electron (-) + Hydrogen (+) —→ AH

  • gain of electrons

oxidation

• accompanied by dehydrogenation (loosing hydrogen)

• loosing electrons

metabolism

two opposing streams of chemical reactions in cells: catabolism and anabolism

catabolism

• Catabolism BREAKS DOWN food and other materials (including damaged cell components)

  • much energy is lost as heat (rest captured in useful forms)

• Into smaller molecules, yielding useful ENERGY and small-molecule BUILDING BLOCKS

  • degradative pathway

• energetically favorable

anabolism

• anabolism (biosynthetic pathways) uses the energy harnessed by catabolism to drive synthesis of molecules that form the cell

• energetically unfavorable

coupled reaction

energy capture is achieved by a coupled reaction

• energetically favorable rxn drives an unfavorable one

• activated carrier or other useful molecule is produced

energy released by a favorable reaction

must be stored temporarily before it can fuel unfavorable reactions such as biosynthesis (anabolism/building things)

• ex: oxidation of a food molecule releases energy

activated carrier

• energy released by favorable rxn can be stored as activated carrier

• small organic molecules holding oe or more energy rich covalent bonds. diffuse rapidly, carrying that energy from sites where energy is made to sites where its used

Activated carriers link what?

anabolism (unfavorable) to catabolism (favorable)

• this is how cells spend activated carriers like money, paying for energetically unfavorable reactions with energy from favorable reactions

Whats the most widely used activated carrier?

ATP

• most important and versatile

• currency of energy for driving many reactions

  • made in an energetically unfavorable phosphorylation

How is ATP made in an energetically unfavorable phosphorylation?

• phosphate group added to ADP, powered by sunlight or breakdown of food

• ATP cycle runs continuously in every cell

NADH and NADPH are the activated carriers of what?

• high energy electrons and hydrogen atoms

• carry energy as two high energy electrons plus a proton (H+) = hydride ion

  • when hydride is passed, a donor molecule oxidizes them to NAD+ and NADP+

NADPH as an electron carrier

• NADPH forms during energy yielding catabolic rxns

  • hydride (H-) ion removed from substrate and added to nicotinamide ring of NADP+

    • typical oxidation-reduction, with substrate oxidized and NADP+ reduced

• NADP+ is the oxidized electron carrier

• NADPH is the reduced electron carrier

Why does NADPH give up its ion readily

giving up the hydride ion btw

• gives it up bc nicotinamide ring has a more stable arrangement of electrons without it

• transfer carries negative free energy charge

How is most ATP made?

• made by mechanisms that first pump protons (H+) across a membrane

oxidative phosphorylation in mitochondria

• uses energy from oxidizing food molecules (taking electrons and hydrogen from stuff like glucose) to drive electron transport

photosynthesis in chloroplasts

• use energy from sunlight to drive electron transport

Oxidative phosphorylation (mitochondria) and photosynthesis (chloroplasts) both do what?

• electron transfer pumps H+, the resulting proton gradient drives ATP synthesis through ATP synthases

making of electrochemical gradient (1)

• electron transport chain embedded in the membrane releases energy (from foods/sunlight) to pump protons (from water) across membrane

making of ATP from ATP synthases (2)

• protons flow back down electrochemical gradient through ATP synthase, which couples the proton movement to ATP production

Chemiosmotic coupling

2 stage membrane based process of generating ATP

• chemi = refers to chemical bond formation of generating ATP

• osmos = (to push), refers to process of pumping protons across membrane

Molecule carried by the electron carriers $\text{NADH}$ and $\text{NADPH}$

A hydride ion ($\text{H}^-$), which consists of two high-energy electrons plus one proton ($\text{H}^+$).

Specific ring structure on $\text{NADP}^+$ that accepts electrons and hydrogen

The nicotinamide ring, which accepts a hydride ion ($\text{H}^-$) during reduction.

Thermodynamic reason why $\text{NADPH}$ readily donates its hydride ion to substrates

The nicotinamide ring reaches a more stable electron arrangement once it loses the hydride ion, resulting in a large negative free-energy change ($-\Delta G$).

Redox state changes during the oxidation of $\text{NADPH}$ by a substrate

• $\text{NADPH}$ is oxidized to $\text{NADP}^+$

• The substrate receives a hydride ion and is reduced

Where did mitochondria and chloroplast come from?

• bacterium (ectosymbiont) lived on outside of an archaeon

• archaeon wrapped around and the membranes fused, enclosing it

• inside as an endosymbiont, it then became the mitochondrion, and new compartments like the nuclear envelope and ER formed around it.

• (chloroplast came later)

proof that mitochondria and chloroplasts were bacteria: (3 things)

still act like bacteria:

• They divide by fission, like a bacterium

• They have their own DNA

• They can make their own RNA and proteins

• double membrane (but not on slides)

structure of mitochondria

• undergo fusion and fission

• dynamic in shape, location, and number

4 parts of the mitochondria

1. matrix

2. inner membrane

3. outer membrane

4. intermembrane space

main purpose of mitochondria

• production of ATP

mitochondria atp production vs glycolysis

• Mitochondria extract about 15 times more ATP from each glucose than glycolysis

• glycolysis nets 2 ATPs for glucose (cytosol)

• mitochondria complete oxidation of same glucose and make 30 ATPs per glucose (CELL RESPIRATION)

3 parts of cell respiration

1. glycolysis

2. citric acid cycle

3. oxidative phosphorylation

glycolysis brief overview

• occurs in cytosol

• breaks glucose into 2 pyruvate

• making 2 ATP and 2 NADH

citric acid cycle brief overview

• Pyruvate → acetyl CoA and enters the loop.

• The loop strips off its carbons as CO₂ (which is what you breathe out)

• The electrons it removes get loaded onto NAD⁺, making NADH.

2 parts of oxidative phosphorylation (last part of cell respiration)

• ETC

• ATP synthesis

electron transport chain (respiratory chain)

• NADH passes electrons down a series of complexes, ending at oxygen to form water

• 3 of the complexes pump protons to build a proton gradient (later used to make ATP)

ATP synthase

Protons get pumped back into matrix and this makes ATP. P + ADP—> ATP

• efficient (100 ATPs per second)

• ancient origin

• reversible: using energy of ATP to move protons uphill (against electrochemical proton gradient) (break down ATP and use that energy to pump protons)

Pyruvate and phosphate import (symport)

• H⁺ flows back into the matrix down the pH gradient and drags pyruvate or phosphate in with it. The matrix needs these for the citric acid cycle and for making ATP.

• proton gradient powers transporters (bring supplies into matrix)

ADP-ATP exchange (antiport):

• ADP goes in and ATP goes out in one exchange.

• The voltage difference across the membrane drives it. The intermembrane side is positive (+++) and the matrix side is negative (---), so negatively charged ATP gets pushed out toward the positive side.

How can electrons move along the ETC?

• Ubiquinones (coenzyme Q, 1st)

• Cytochrome C (2nd)

Like for any carrier, reduced when it receives electrons from the carrier before it and oxidized when it hands those electrons to the next carrier.

Ubiquinones

(coenzyme Q, 1st)

• membrane embedded mobile electron carriers (hydrophobic molecules, NOT proteins)

Cytochrome C

(2nd)

• A small, peripheral protein in intermembrane space

• Also mobile electron carriers (a protein, using metal such as heme to bind electrons)

• Covalently linked via two thioether bonds

Cytochrome C oxidase

(final carrier)

• Removes electrons from cytochrome c

• High electron affinity due to presence of a heme group and a copper atom at the oxygen binding site.

What happens to electrons’ energy in the ETC?

Electrons lose free energy in small steps as they move to carriers with higher electron affinity (NADH → O₂). The energy released at Complexes I, III, and IV pumps H⁺ across the membrane, building the gradient that drives ATP synthase.

Which way do electrons flow in the ETC, and why?

From low to high redox potential (measure of how strongly a molecule wants to gain electrons)

• (NADH → O₂),

• because it’s energetically favorable (-ΔG).

• Low redox potential = low electron affinity = e donor.

• High = high affinity = e acceptor.