Energy in Cells

Metabolism

totality of an organism’s chemical reactions

Metabolic pathway

a specific molecule is altered in a series of steps to produce a product; Each step is catalyzed by a specific enzyme

Enzyme

a macromolecule that speeds up a specific reaction

Anabolic pathways/Anabolism

consume energy to build complex molecules from simpler ones; “uphill” reactions; endergonic

ex. Synthesis of protein from amino acids

Catabolic pathways/Catabolism

release energy by breaking down complex molecules into simpler compounds; “downhill” reactions; exergonic

ex. Cellular respiration, the breakdown of glucose in the presence of O₂

Autotrophic

self-sufficient; Energy to support life comes from sunlight or inorganic matter

ex. plants

heterotrophic

eat other organisms; Energy to support life comes from organic carbon sources, and originates with autotrophs

Oxidation of glucose

major source of energy for animals, Organic molecules store energy that can be released by oxidation

Free energy (G)

the amount of energy available to do work; Chemical bonds store both potential energy (heat/enthalpy), and order
ΔG = ΔH - TΔS

Enthalpy

Total energy stored in a chemical bonds in the system.

Entropy

“Disorder” that is prevented by the bonds.

Exergonic

Negative ∆G reaction is spontaneous (releases energy

Endergonic

Positive ∆G reaction is not spontaneous (consumes energy)

Aerobic oxidation/glucose catabolism

exergonic

reverse reaction of photosynthesis

Photosynthesis

endergonic

reverse reaction of aerobic oxidation

spontaneous combustion of glucose

∆G for this reaction is large and negative (-686 kcal/mol), thus theoretically possible; but high activation energy

thermodynamically favourable, but kinetically unfavourable

catalyst

lowers the activation energy of a reaction; ∆G does not change

activation energy

Activation energy is ∆G between reactants and transition state

coupling

pairing of an exergonic reaction with an endergonic reaction; Couple an unfavorable reaction to one with a greater (absolute) ∆G, we can drive it forward

ex. Hydrolysis of ATP & changing conformation of a protein

closed system equilibrium

reaches equilibrium then does no work

open system equilibrium

flow in and our prevents complete equilibrium, enabling cels to continue work

Chemical wor

pushes endergonic reactions

Transport work

pumps substances across membranes against the direction of spontaneous movement, active transport

ex. Na+/K+ pump

Mechanical work

beating cilia, contracting muscle cells

synthesis of ATP

coupled to exergonic reactions (e.g. oxidation of glucose)

Breakdown of ATP

can be coupled to endergonic reactions, driving them forward; rechargeable

NADH

another ‘battery’; stores “reducing power”

ATP (adenosine triphospate)

nucleic acids with three linked phosphate groups; High energy phospo-anhydride bonds; three closely juxtaposed negative charges that ”want to be” further apart; hydrolysis release energy

phosphorylated intermediate

phosphate provided by ATP hydrolysis that modifies the reactant

Enzymes

macromolecule (typically protein) that acts as a catalyst to speed up a specific reaction; name often ends in -ase

Active site

region on the enzyme, often a pocket or groove, that binds to the substrate

Enzyme strategies

• Orienting substrates correctly for reaction

• Straining bonds in the substrate

• Directly stabilizing the transition state

• Providing a favorable microenvironment (e.g. hydrophobic pocket)

• Forming an intermediate that is covalently bonded to the substrate

Substrate

reactant that an enzyme acts on

enzyme-substrate complex

the complex when an enzyme binds to the substrate

multiple turnover

an enzyme can catalyse many substrates; must be able to capture and release

induced fit

Binding of substrate to enzyme is exergonic (new hydrogen bonds, etc), and can change the conformation of the enzyme to better accommodate the substrate; Brings the chemical groups of the active site into positions that enhance catalysis of the reaction; The substrate is typically held in the enzyme’s active site by weak bonds, such as hydrogen bonds

Optimal conditions

Enzyme activity can be regulated by temperature, pH, concentration of ions, etc.

Competitive inhibitors

bind the active site (i.e. compete with substrates)

Non-competitive/allosteric inhibitors

bind elsewhere and change the conformation of the enzyme to prevent substrate binding or reaction

Allosteric regulation of enzyme activity

Allosteric interactions can inhibit or activate enzymes; Enzyme has an active and an inactive conformation. When the regulator binds to the enzyme, it stabilizes one of these.

methotrexate

competitively inhibits dihydrofolate reductase, which ultimately inhibits DNA synthesis; cancer + autoimmune treatment

omeprazol

gastricitis/acid reflux medication; inhibits H+/K+-ATPase; inhibition of gastric juice secretion

Zidovudine (AZT)

anti-HIV drug; Nucleoside analog reverse transcriptase inhibitor

Feedback inhibition

the product of a biosynthetic pathway inhibits the first enzyme in the pathway, preventing wasteful synthesis of a product when it is already abundant; cell can then divert the precursor molecules to other pathways

sildenafil citrate

inhibits phosphodiesterase; GMPc accumulation