Ch 6: Metabolism

where does the energy that sustains most of the earth’s life forms comes from?

the sun

bioenergetics

study of energy flow through a living system

metabolism

all chemical reactions of a cell or organism

metabolic pathway

series of biochemical reactions that converts one or more substrates into a final

2 types of reactions/pathways required to maintain cell’s energy balance

• anabolic

• catabolic

anabolic metabolic pathways

small molecules are assembled into large ones. energy is required.

catabolic metabolic pathway

large molecules are broken down into small ones. energy is released

energy

ability to do work

• objects in motion have kinetic energy

• objects that have the potential to move have potential energy

chemical energy

energy stored in chemical bonds (potential) then released (kinetic)

bioenergetics of a system

the amount of energy exchanged in metabolic reactions

gibb’s free energy (G)

the amount of energy available to do work (usable energy)

• all chemical reactions affect G

• ΔG = change in G after a reaction

ΔG = ΔH-TΔS

• ΔH = change in total energy of the system (enthalpy)

• T is the temperature in Kelvins (^oC + 273)

• ΔS is change in entropy (energy lost to disorder)

exergonic reactions

energy is released in a chemical reaction

• ΔG < 0

• products will have less free energy than substrates

• are spontaneous because they can occur without addition of energy (reactants are enough)

  • spontaneous reactions do not necessarily occur quickly

endergonic reactions

chemical reaction required an input of energy

• ΔG > 0

• products will have more free energy than substrates

• not spontaneous/ will not occur quickly

activation energy

the energy required for a reaction to proceed

1. causes reactant(s) to become contorted and unstable, allowing bond(s) to be broken or made

2. unstable state is called the transition state

3. in transition state the reaction occurs very quickly

what is the main source for activation energy in a cell?

heat energy

• helps reactants reach transition state

thermodynamics

study of energy and energy involving physical matter

first law of thermodynamics

the total amount of energy in the universe is constant

• energy cannot be created or destroyed

second law of thermodynamics

the transfer of energy is not completely efficient

• in chemical reactions some energy is lost and unusable (i.e. heat energy)

  • increases entropy (disorder)

    • cell has to work harder to keep order: hard to maintain order in the face of disorder

ATP: adenosine triphosphate

provides the energy for a cell’s endergonic reactions

ATP structure

composed of adenosine backbone with 3 phosphate groups attached

• adenosine = nitrogenous base adenine + 5-carbon ribose

• 3 phosphate groups: alpha, beta, and gamma

  • more phosphates → more unstable → easier to break

• bonds between phosphate groups are high-energy

  • when broken the products have lower free energy than reactants

ATP hydrolysis

• ΔG = -7.3 kcal/mol (nearly double in cells)

• ATP is unstable and hydrolyzes quickly

• energy lost as heat if not coupled to endergonic reaction

• when coupled with an endergonic reaction much of the energy can be transferred to drive that reaction

• ATP hydrolysis is reversible

the sodium-potassium pump

enzymes

• primarily protein catalysts that speed up reactions by lowering the required activation energy

• bind with reactants and promote bond-breaking and bond-forming processes

• very specific, catalyzing a single reactions

• do not change reaction’s ΔG

• enzymes are specific to actions → big metabolic forces need a lot of enzymes

enzyme-substrate specificity

• 3d shapes (enzyme and substrates) determine specificity

• substrates interact at enzyme’s active site

• enzymes can catalyze a variety of reactions

3d image of enzyme active site

• protein structure: scaffold to support and position active site

• active site

  • binding sites: bind and orient substrate(s)

  • catalytic site: reduce chemical activation energy

enzyme induced fit

• at active site, a mild shift in shape optimizes reactions

• slight changes maximize catalysis

• enzyme remains unchanged following reaction (resets)

protein structure revisited

• 3d shape of protein determined by amino acid sequence

• AAs of active site important for enzyme’s function - allow binding with unique substrates

• cellular environment important enzyme function

what are important considerations for the cellular environment for enzyme function?

1. suboptimal temperatures can denature the enzyme (loss of shape)

2. suboptimal pHs can reduce substrate-enzyme binding

• lower temp slows down reactions b/c enzymes are moving slower

• increased temp denatures enzymes to tertiary or secondary structure

  • fever: temp is raised just enough to speed up the immune system

lowering activation energy

an enzyme can help the substrate reach its transition state in one of the following ways

1. position two substrates so they align perfectly for the reaction

2. provide an optimal environment (i.e. acidic, polar) within the active site for the reaction

3. contort/stress the substrate by destabilizing the bonds so it is less stable and more likely to react

4. temporarily react with the substrate (chemically change it) making the substrate less stable and more likely to react

enzyme regulation

helps cells control environment to meet their specific needs

how can enzymes be regulated?

1. modifications to temperature and/or pH

2. production of molecules that inhibit or promote enzyme function

3. availability of coenzymes or cofactors

4. regulate expression at DNA level (transcription/translation)

what are the 2 ways to inhibit enzymes?

through competitive inhibitors and noncompetitive inhibitors

competitive inhiibitors

have similar shape to substrate and compete w/ substrate for active site

noncompetitive inhibitors

bind to enzyme at different location (allosteric site) and slows reaction rate

enzyme inhibition

• competitive inhibition slows reaction rates but does not affect the maximal rate

• noncompetitive inhibition slows rates and reduces the maximal rate

• maximal rate: speed of a reaction when substrate is not limited → saturation: all active sites are taken up

allosteric inhibitors

modify active site = substrate binding is reduced or prevented

allosteric activators

modify active site = affinity for substrate increases

enzyme cofactors

some enzymes require 1 or more cofactors or coenzymes

• cofactors: inorganic ions

• coenzymes: organic molecules and vitamins

• obtained primarily from diet

feedback inhibition in metabolic pathways

end-product of pathway inhibits an upstream step

• important regulatory mechanism in cells

  • ex. ATP allosterically inhibits some enzymes involved in cellular respiration