Cell Metabolism

cell metabolism

• organism selection: need the right one for the job

  • cell has to efficiently make the product

  • genetic engineering allows engineers to add/remove genes to alter metabolic functions

• differences in microbial metabolism due to:

  • genetic differences

  • differences in response to environment

• example: S. cerevisiae

  • anaerobic = ethanol

  • aerobic = baker’s yeast

• two key concepts:

  • catabolism: degrading a compound to smaller and simpler products

    • glucose to CO2 and H2O

  • anabolism: synthesis of more complex compounds

    • glucose to oxygen

ATP

• how energy in biological systems is stored and transferred

  • contains high energy phosphate bonds

• analog compounds of ATP also store and transfer high energy phosphate bonds

  • GTP

  • UTP

  • CTP

cellular energetics

• ATP is needed in cells to drive energetically unfavorable reactions

• eukaryotic cells use specialized membranes inside of energy-converting organelles (mitochondria) to produce most of their ATP

• prokaryotic cells produce ATP in cytosol via glycolysis and in the cell wall

ATP:ADP ratios

• ATP:ADP ratio within the cell must stay high

  • the ATP pool is used to drive energetically unfavorable reactions

  • if ATP levels begin to fall, energetically unfavorable reactions cease, the cell die

    • cyanide - blocks electron transport in the inner mitochondrial membrane

• the ATP:ADP ratio must remain high

  • deltaG = deltaG0 + RT*ln{[ADP][Pi]/{ATP]}

  • at low [ATP], deltaG approaches zero

  • at low [ATP] many biosynthetic reactions wound begin to run backwards

glucose metabolism

• glucose is the major energy source for many organisms

• aerobic catabolism of glucose has three phases

  • embden-meyerhof-parnas (EMP) pathway transforms glucose to pyruvate

  • citric acid cycle for conversion of pyruvate to CO2 and NADH

  • ETC for formation of ATP

    

mitochondria

• occupy a large fraction of the cytoplasmic volume

• essential for the evolution of higher eukaryotes

  • metabolism of sugars by mitochondria produces 15 times more ATP than glycolysis

• enclosed by two specialized membrranes

  • outer membrane contains porin molecules to transport small molecules

  • inner membrane contains:

    • phospholipid cardiolipin: makes membrane especially impermeable to ions

    • transport proteins that transport molecule needed for enzymes within the matrix

  • matrix includes enzymes that metabolize pyruvate and fatty acids to produce acetyl CoA and those that oxidize acetyl CoA in the citric acid cycle

citric acid cycle

• mitochondria use both pyruvate (glucose and other sugars) and fatty acids (fats) for fuel

• pyruvate and fatty acids are transported across the inner mitochondrial membrane and converted to acetyl CoA by matrix enzymes

• acetyl CoA is converted (via the citric acid cycle) to CO2 and high energy electrons

  • high energy electrons are carried by the activated carrier molecules NADH and FADH2

  • electrons are transferred to the inner mitochondrial membrane

  • NAD+ and FAD are regenerated

• the CAC is considered part of aerobic metabolism, but does not use O2

• the major roles of the TCA cycle are

  • to provide electrons for electron transport chain

  • supply C skeletons for AA synthesis

  • generate energy

respiration

• in the final catabolic reactions on the inner mitochondrial membrane, O2 is used

  • electrons transferred by NADH and FADH2 to O2 through a series of electron carriers

  • ATP is formed

chemiosmotic coupling

• common pathway used by cells to harness energy

  • chemical bond forming reactions that form ATP (chemi)

  • membrane transport process (osmotic)

• occurs in two stages:

  • stage 1: high energy electrons are transferred between electron carriers embedded in the membrane; electron transfers release energy that is used to pump protons across the membrane and generate an electrochemical proton gradient

  • stage 2: H+ flows down its electrochemical gradient through ATP synthase (acts like a turbine), which catalyzes the synthesis of ATP from ADP and inorganic phosphate

electron transport chain

• composed of both the membrane proteins and small molecules involved in electron transfer

  • in biological systems, electrons are carried from one site to another by diffusible molecules

  • mitochondria use NAD+, which picks up two electrons and an H+ molecule to form NADH

biological oxidation

• respiratory chain harvests energy from the energetically favorable reaction: H2 +1/2O2 → H2O

  • reaction happens in many small steps so most of the released energy can be stored instead of lost as heat

  • hydrogen atoms are first separated into protons and electrons

  • electrons pass through a series of electron carriers in the inner mitochondrial membrane

  • at the end of the ETC protons are returned permanently when they neutralize the oxygen molecule

• electron transport begins when the hydride ion is removed from NADH

  • converted to a proton and two electrons

    • H- → H+ + 2e-

  • the two electrons are passed to the first of many different electron carriers in the respiratory chain

    • primarily passed from one metal ion to another

    • metal ions are bound to transmembrane proteins that alter the affinity of the metal ions for electrons

    • each metal/protein complex in the chain has a greater electron affinity than the last

    • final transfer is to oxygen, which has the greatest electron affinity

  • electrons start with very high energy and gradually lose energy as the pass along the chain

energy storage

• the energetically favorable transfer of electrons is coupled to:

  • oriented H+ uptake and release

  • allosteric changes in energy-converting protein pumps

• the net result is H+ pumping across the inner membrane (from the matrix to the intermembrane space)

  • driven by the energetically favorable flow of electrons

• two consequences:

  • a pH gradient is generated

    • pH 7.5 in matrix, pH 7.0 in intermembrane space

  • a voltage gradient is generated across the inner mitochondrial membrane

    • negative within matrix, positive within intermembrane space

electrochemical proton gradient

energy generating metabolism summary

ATP synthesis

• the electrochemical proton gradient across the inner mitochondrial membrane drives ATP synthesis

• ATP synthesis is performed by the membrane-bound enzyme ATP synthase

  • creates a hydrophilic pathway across the inner membrane that allows H+ passage down the electrochemical gradient

  • can also reverse to hydrolyze ATP and pump H+

proton gradient transport

• the electrochemical proton gradient drives several other processes:

  • transport of charged molecules into the matrix

    • pyruvate

    • inorganic phosphate

• ADP and ATP are co-transported in opposite directions by a single transporter

  • ATP has one more negative charge than ADP, voltage differences across membrane drives transport

redox potential

• measure of electron affinities

  • the tendency for redox reactions to move forward (for an electron to be removed from one molecule and added to the next) depends on the free energy change (deltaG) for the electron transfer

  • deltaG depends on the relative affinities of the two molecules for electrons

• redox pairs: pairs of compounds that can transfer electrons

  • NADH ←> NAD+ + H+ +2e-

  • NADH is a strong electron donor, therefore NAD+ is a weak electron acceptor

• can measure the redox potential of redox pairs

  • need an electrical circuit linking a 1:1 mixture of one redox pair to a second redox pair that can act as a reference standard

  • measure the voltage between them

  • voltage difference = redox potential

• NADH/NAD+ = low redox potential

  • low affinity for electrons, good molecule for donating electrons

• O2/H2O = high redox potential

  • high affinity for electrons, good molecule to act as a “sink” for electrons at the end of the pathway

electron transfers release energy

• 1:1 mixture of NADH/NAD+ has a redox potential of -320 mV

• 1:1 mixture of O2/H2O has a redox potential of +820 mV

• transfer of an electron from NADH to O2 has a free energy change of deltaG0 = -26.2 kcal/mol

• huge free energy drop means most energy would be lost as heat

• stepwise process allows cells to store almost half of energy released

anaerobic metabolism

• anaerobic respiration: production of energy in the absence of oxygen

  • alternative electron acceptor

  • nitrate

• growth without using the ETC = fermenration

  • organic substrate undergoes a balanced series of oxidative and reductive reactions

  • end product formed in response to the cell’s need to balance consumption and production of reducing power

fermentation

autotrophic metabolism

• heterotrophic growth: organic molecules serve as carbon energy sources

• autotrophic growth: energy for growth can be supplied by CO2

  • photoautotroph: light

  • chemoautotroph: oxidation of inorganic chemicals

aerobic and anaerobic metabolism

cell growth