Metabolic Pathways pt 1; Catabolic Pathways

Catabolic Pathways

Release energy by breaking down complex molecules into simpler compounds

Aerobic Respiration

Oxygen is consumed as a reactant along with organic fuel

Anaerobic Respiration

Organic fuel is broken down without oxygen

Fermentation

Partial breakdown of organic fuel (sugars) without oxygen

Cellular Respiration

Aerobic (and anaerobic) respiration

• exergonic

Redox

The transfer of electrons from one molecules to another. Always coupled!

Reducing Agent

Molecules that gives up electrons and becomes oxidized

Oxidizing agent

Molecule that receives electrons and becomes reduced

Combustion of Methane

C-H and O-O bonds:

• e- shared equally

• Higher potential energy reactants

• Less energy to break

• H+ and e- get transferred from CH4 to O2

C=O and O-H bonds:

• e- shared unequally

• C is oxidized

• Unequal e- sharing makes bonds more stable

• More energy is released when formed, more energy is required to break bonds (photosynthesis)

Nicotinamide adenine dinucleotide (NAD+)

Is an electron transporter (“shuttle”)

• Facilitates the electron transfer over multiple steps in the breakdown of glucose

• It’s a coenzyme and oxidizing agent

• It can cycle between an oxidized (NAD+) and reduced (NADH) form

Electron Transport Chain

• IF the transfer of electrons was uncontrolled

  • One big release of energy, with LOTS of heat loss

• IF controlled by the cell

  • Small releases of energy at each step, which can be used to make more ATP

  • e- get removed from glucose and are transferred to the ETC

Substrate-level phosphorylation

• An enzyme catalyzes the transfer of a phosphate group from a substrate to ADP, forming ATP

• The substrate is generated as an intermediate in the breakdown of glucose

• Direct transfer of energy to ATP

• Accounts for about 10% of ATP generation during cellular respiration

• Occurs in the cytosol and mitochondria

Oxidative phosphorylation

• Energy is released from electrons in the ETC makes a H+ gradient

• This gradient is used to drive a protein complex called ATP synthase

• Indirect transfer of energy to ATP

• Makes approx. 90% of ATP during cellular respiration

• Mitochondria only

Overview of Cellular Respiration

Glycolysis (SLP ATP) → Pyruvate Oxidation → Citric Acid Cycle (SLP ATP) → Oxidative Phosphorylation (OP ATP)

Glycolysis

Means “sugar-splitting”

• Glucose (6-carbon sugar) is split into two 3-carbon sugars

• No loss of carbon

Pyruvate

Actively transported to the mitochondrion after glycolysis which is then converted to acetyl CoA.

Pyruvate —> acetyl CoA

1. Oxidized carboxyl group is removed

2. The 2-carbon molecule is oxidized forming acetate (CH3COO-)

3. Coenzyme A (S-CoA) attaches by its sulphur group

The Citric Acid Cycle (AKA Krebs Cycle, Tricarboxylic Acid cycle (TCA))

• Generates 1 ATP molecule per cycle via substrate-level phosphorylation

• Most energy is transferred to NAD+ and FAD which shuttle electrons to the ETC where most of the energy will be produced

Total Yield per glucose

Since each glucose at the start of glycolysis yield 2 acetylene CoA, the total yield per glucose is:

6NADH’s , 2FADH2’s, 2ATP’s

Electron Transport Chain (ETC)

A collection of protein complexes within the inner membrane of the mitochondrion

• Sequential redox rx

• Every component becomes reduced when it accepts electrons from its uphill neighbour, since the electronegativity (ability to attract electrons) is less than downhill

ETC complex I

Electrons acquired from glycolysis and the citric acid cycle via NAD+ are transferred from NADH to the ETC complex I.

• The first molecule in complex I is a flavoprotein (flavin mononucleotide (FMN)) which gets reduced as NADH give up its electrons

• FMN returns to its oxidized form as it passes the electrons to iron-sulfur protein in complex I

• Electron then moves to ubiquinone (Q) — not a protein (AKA coenzyme Q)

• Next, electrons are transferred to the cytochromes

  • Proteins consisting of an iron group the accepts/donates electrons

  • Complexes III and IV both have cytochromes

• The cytochromes then pass the electron to molecular oxygen which picks up 2e and 2 protons (Hydrogen) to form water

ETC complex II

Electrons acquired from the citric acid cycle via FADH2 undergo a similar process

KEY difference: it joins the ETC via complex II

• Lower E level than complex I and NADH

• Both donate the same number of electrons at the end for oxygen reduction but FADH2 converts about 1/3 less energy than NADH.

• NADH > FADH2

ATP synthase

A protein complex that is found throughout the inner membrane of the mitochondrion

• Makes ATP from ADP + inorganic P

• Oxidative Phosphorylation

• Works like an iron pump but reverse

Stator

A channel anchored in the membrane, which H+ ion can flow down their concentration gradient. (High → Low)

• Entrance, Step 1

Rotor

H+ ions enter binding sites in the rotor changing the shape of the protein subunit so that it spins (like a centrifuge).

• Constant influx of H+ atoms

Each H+ ion must make ONE COMPLETE turn before going through a second channel in the stator and into the mitochondrial matrix

Rod and Knob

Rotor causes the rod to spin, which extends into a knob held stationary by the stator.

Turning off the rod activates catalytic sites that produce ATP from ADP in he knob

ETC effect on the H+ gradient

Since ETC is exergonic, energy is used to pump H+ ions from the mitochondrial matrix to the inter-membrane space (space between the inner and outer mitochondrial membranes).

H+ ions then diffuse back into the mitochondrial matrix via the ATP synthase which produces a proton-motive force

Chemiosmosis

ATP synthesis powered by the flow of H+ back across the membrane

• an energy coupling mechanism

  • Uses energy stored from H+ gradient across the membrane to drive cellular work

Anaerobic respiration

Respiration in which the final e- acceptor is not oxygen

• Still contains an ETC but the final e- acceptor is different

  • Species specific → some sulphate-reducing bacteria use SO4^(-2)

  • Produced hydrogen sulphide as a byproduct instead of water

Fermentation

Does not have an ETC or oxygen as the final e- acceptor

• NOT cellular respiration

Alcohol fermentation

Pyruvate is converted to ethanol

1. CO2 is released from Pyruvate, converting it into 2 molecules of acetaldehyde

2. Acetaldehyde is reduced by NADH to ethanol

• This regenerates the NAD+ needed in glycolysis

• Many bacteria do this

• Also yeast

• Sourdough or beer

Lactic acid fermentation

• Pyruvate is reduced directly by NADH to form lactic acid

• No release of carbon dioxide

• Fungi

• Bacteria → cheese and yogurt

Obligate Anaerobes

Organisms that only carry out fermentation or anaerobic respiration

• HAVE to be in O2 free environment

• Only fermentation

Facultative Anaerobes

Organisms can utilize both fermentation and cellular respiration to make enough ATP.

• Prefer cellular respiration but can fermentation