energy is the capacity to do work potential energy: stored energy kinetic energy: energy of motion

Energy is the capacity to do work

• Potential energy: stored energy

• Kinetic energy: energy of motion

Metabolism• Metabolism is the

sum total of ALL chemical reactions within a cell– Catabolic– Anabolic /

Biosynthetic

A metabolic pathway is a series of sequential, interconnected,

enzyme-catalyzed biochemical reactions by which a living cell

converts a starting product (substrate) into an end product.

Metabolism

• Catabolism: “destructive metabolism”– Breakdown of substrate:

end product is less complex than the starting product

– Catabolic pathways generate energy and precursor metabolites

– Catabolic pathways are linked to either respiration or fermentation

• Anabolism = biosynthesis: “constructive metabolism”– Synthesis of new

biomolecules: end product is more complex than the starting product

– Anabolic pathways use energy and precursor metabolites to synthesize subunits of macromolecules

Adenosine triphosphate: ATP• The main energy currency of the cell• Ribose + adenine + 3 phosphate groups• Phosphate bonds = high energy bonds: energy is used to form

the bonds and released when the bonds are broken• Addition of a phosphate group to ADP to generate ATP is

accomplished during metabolism via either substrate level phosphorylation or oxidative phosphorylation

And microorganisms too!

ATP is made in catabolic reactions and used in anabolic

reactions

Ways cells make ATP

• Substrate level phosphorylation – used by all organisms; for fermenters, this is the only option

• Oxidative phosphorylation – aerobic and anaerobic respiration

• Photophosphorylation – photosynthesizers only

Products of Anabolic Metabolism (Biosynthesis)

• Fatty acids• Glycerol

– Fatty acids + glycerol = lipids

(where do you find lipid in a bacterial cell?)

• Amino acids– Building blocks for

proteins

• Nucleotides– Building blocks for

DNA, RNA

The critical components of metabolic pathways are:

• Enzymes• Adenosine triphosphate (ATP)• Chemical energy source• Terminal electron acceptor• Electron carriers

Oxidation-Reduction Rections (redox reactions)

• Same principal in biological systems as inorganic systems:– Substance that gives up (loses) electron(s) =

oxidized– Substance that gains electron(s) = reduced

• When electrons move, protons (H+) follow

Oxidation/reduction reactions

Biological Oxidation

Enzymes• All enzymes are proteins• Active site = binding site: highly substrate-specific• Binding of the substrate induces a conformational change

in the enzyme – This forms the temporary enzyme-substrate complex– Formation of this complex changes the position of bonds on the

substrate, destabilizing them and thereby lowering the activation energy of the reaction

• When the changed substrate is released, the enzyme returns to the native conformation and is ready to bind another substrate – the enzyme is chemically unchanged by the reaction.

Enzymes

• Active site: site that binds the substrate• Allosteric sites: binding site at a location separate from the active

site – binding to the allosteric site can induce a conformational change in the active

site

• Allosteric regulation: binding of a molecule to the allosteric site to either allow or block binding of the substrate– This allows the cell to regulate pathways based on the quantity of the end

product available, so they only make what they need

• Coenzymes: organic cofactors that assist in the transfer of molecules or electrons

• Environmental factors that influence enzymatic function/activity:

– temperature, pH, salt concentration

Factors that influence an enzyme: Temperature

• What happens as temperature increases?

• What is the optimum temperature?

Factors that influence an enzyme: pH

• What pH do most enzymes function optimally?

Enzymes bind substrate and generate a product

Some enzymes require a cofactor to bind substrate

Coenzymes carry electrons

Enzyme inhibitors

• Inhibit the binding of the substrate to the active site– Competitive inhibition– Non-Competitive Inhibition

Competitive Inhibition

Non-competitive Inhibition

Electron carriers

• Special types of coenzymes that transfer electrons (and protons) between molecules

• NAD+/NADH: nicotinamide adenine dinucleotide• NADP+/NADPH: nicotinamide adenine dinucleotide phosphate• FAD/FADH2: flavin adenine dinucleotide

Electron Transport Chain & Proton Motive Force

• The ETC is an association of electron carriers located within a cell membrane.

• As electrons pass between electron carriers in the ETC they move from higher to lower affinity carriers, releasing energy in the process.

• Movement of electrons is paired with the movement of protons across the membrane to generate an electrical gradient

• This electrical gradient = the proton motive force.

• It consists of a positive charge at the outside surface of the membrane and a negative charge at the inner surface

• The electrical potential energy of the proton motive force can be converted to chemical energy = production of ATP

The Electron Transport Chain and the Proton Motive Force: Prokaryotic vs eukaryotic cells

• Prokaryotic cells:– Electron transport chain is located

in the cytoplasmic membrane– Electrical gradient of the proton

motive force is across the cell membrane (inside vs outside cell)

– Proton motive force can be used to generate ATP, or to directly power flagella or transport molecules against the concentration gradient (active transport)

• These latter 2 processes can also be fueled by ATP generated via the proton motive force

• Eukaryotic cells:– ETC is located in the inner

mitochondrial membrane– Electrical gradient of proton

motive force is between the matrix and the region between the inner and outer membranes

– Only function of the proton motive force is generation of ATP

Central metabolic pathways: catabolic pathways

• Glycolysis: primary pathway for most organisms

• Substrate = glucose• End product =

pyruvate

• The other pathways are the pentose phosphate pathway and the tricarboxylic acid pathway – these are linked by a “transition step”

Types of Bacterial Metabolism

• Fermentation• Respiration

– Aerobic Respiration– Anaerobic Respiration

• Photosynthesis

Comparison of three types of metabolism

make a new slide to replace this = a table summarizing what I want them to know = name of the process, pathways used, terminal electron accentor and “energy yield” – substrate level + phosphorylation and oxidative phosphorylation – need a slide summarizing

the difference between these two – also a note on this slide saying I just want them to know that for both SLP and OP the energy yielod is greatest for aerobic respiration, lowest for fermentation and intermediate for anaerobic respiration; and also that in

fermentation there is ONLY substrate level phosphorylation, not oxidative phosphorylation

Cellular Respiration• The series of steps by which cells produce

energy through oxidation of organic substances

• At a cellular level, this can be linked to catabolism – electrons extracted in the metabolism of glucose (or other substrates) are transferred to the electron transport chain to generate ATP via oxidative phosphorylation

Respiration

• Aerobic respiration:– Uses ETC– Oxygen is the terminal

electron acceptor– ATP is generated by both

substrate level and oxidative phosphorylation

– Higher energy yield than anaerobic respiration or fermentation

• Anaerobic respiration:– Uses ETC– Terminal electron

acceptor = various molecules other than O2, ie nitrate, nitrite, sulfate

– ATP is generated by both substrate level and oxidative phosphorylation

Aerobic Respiration

• The COMPLETE breakdown of glucose to CO2 and H2O with an inorganic compound serving as the final electron acceptor

Remember the pathways in aerobic respiration are…

• Glycolysis– Some use Pentose Phosphate Pathway instead

• TCA cycle• Electron transport chain

Fermentation

• The incomplete breakdown of glucose with an organic compound serving as the final electron acceptor

• Generates less energy than aerobic or anerobic respiration

• Only central metabolic pathway operating is glycolysis

• Question: if fermentation is so inefficient, why do cells use this pathway?

Fermentation products can vary

Fermentation

Saccharomyces produces ethanol

Lactic Acid Bacteria

Precursor metabolites• There are many important precursor metabolites

formed during the central metabolic pathways which are used in biosynthetic (anabolic) pathways. – Fructose 6-phosphate

• Generated during glycolysis• Used in the synthesis of peptidoglycan

– Glucose 6-phosphate• Generated during glycolysis• Used in the synthesis of lipopolysaccharide

Carbon fixation

• Organism that are able to use CO2 as a carbon source =

• Pathways utilized include Calvin Cycle and reverse TCA cycle

• Some bacteria are able to break down CO2 to yield carbon

Chemoorganotrophs depend on Photosynthetic organisms

What is made as a result of the TCA cycle?

• ATP• Reducing power• Precursor metabolites made from alpha-

ketoglutarate and oxaloacetate

Electron Transport Chain

• Found in the cytoplasmic membrane• Contains electron carriers

– Flavoproteins– Iron-sulfur proteins– Quinones– Cytochromes

Model for energy release in ETC

ETC in eukaryotes

ETC in prokaryotes

ATP yield from aerobic respiration

Remember we are focusing on catabolic reactions

• Generate ATP for later use by cell• Generate precursors for other pathways• Need to re-oxidize coenzymes for continual

use