gen bio - lecture 7: metabolism

metabolism

the totality of all chemical reactions + energy transformations occurring within an organism

• essential reactions for maintaining life, growth, reproduction, homeostasis

• emergent property of life (arises from the coordinated interaction of many molecular components within cells)

metabolic pathways (define + LIST two types)

• a series of stepwise chemical reactions, each catalyzed by a specific enzyme, that transform a starting molecule into a final product

  • regulated and controlled to optimize energy + maintain cellular balance + maintain homeostasis

    • regulation ensures that energy and resources are used efficiently + products are synthesized only when needed

2 types…

• anabolic pathways

• catabolic pathways

anabolic pathways/anabolism (definition, energy, examples, general formula)

• definition: pathways that build complex molecules from simpler ones

• energy: requires input of energy (endergonic)

• examples:

  • protein synthesis from amino acids

  • DNA replication

  • photosynthesis

• general reaction:

  • simple molecules —> complex molecules

catabolic pathways/catabolism (definition, energy, examples, general formula)

• definition: pathways that break down complex molecules into simpler ones

• energy: release energy (exergonic), often stored in ATP

• examples:

  • cellular respiration

  • digestion of macromolecules

• general reaction:

  • complex molecules —> simpler molecules

energy (general definition and define kinetic + potential)

• energy: the capacity to cause change or do work

  • exists in different forms + can be transformed from one form to another

• kinetic energy: energy of motion

  • ex. moving molecules, flowing water

• potential energy: stored energy based on position/structure

  • ex. chemical bonds in glucose, water behind a dam

first law of thermodynamics

energy cannot be created or destroyed, only transformed from one form to another

• total energy in a closed system (ex. universe) is constant

• ex. food contains chemical energy —> converted to heat and ATP

second law of thermodynamics

every energy transformation increases the entropy (a measure of disorder or randomness) of the universe

• some energy = unusable so released as heat

• no energy transformation = 100% efficient

  • ex. of inefficiency: car engine, cellular respiration

4 steps of the energy flow in ecosystems

1. light energy enters from the sun

2. converted by plants (photosynthesis) into chemical energy

3. heat energy is lost @ each step; it exits the ecosystem

4. total energy remains constant BUT energy available to do work increases

gibbs free energy (+ exergonic/endergonic reactions)

• definition: energy in a system that is available to do work

  • cannot directly be measured BUT the change in free energy can be measured during a reaction

ΔG < 0 - exergonic, energy released, spontaneous

ΔG > 0 - endergonic, energy absorbed, not spontaneous

ΔG = 0 - no work done, system @ equilibrium, no net change

ATP structure + function

• function: main energy carrier used by cells to perform work

  • used by cells to store, transfer and release energy as needed for biological processes

• structure (3 components):

  • ribose (5 carbon sugar)

  • adenine (nitrogenous base)

  • 3 phosphate groups linked by high-energy bonds

    • bonds between these groups = “spring loaded” due to the instability and high energy stored there inside of the bond

ATP hydrolysis

ATP —> ADP + Pi + energy

• exergonic reaction

coupled reactions

• occur when an exergonic reaction is used to drive an endergonic reaction

  • ex.

    • exergonic (ATP hydrolysis)

    • endergonic (building macromolecules)

      • these reactions often occur simultaneously + are linked to make non-spontaneous processes possible

phosphorylation (definition + 4 steps of process)

• definition: the transfer of a phosphate group from ATP to another molecule

• this process…

1. uses ATP hydrolysis to release a phosphate group (ADP + Pi)

2. attaches the phosphate to a reactant or protein

3. causes a shape change in the target molecule

4. changes the molecule’s function (often activates it or makes it more reactive)

phosphorylated intermediate

molecule that receives the phosphate

• usually higher in energy + more likely to participate in a chemical reaction

enzymes (definition + how they work general def)

• biological catalysts (usually proteins) that speed up chemical reactions in cells

  • do NOT get consumed or permanently altered in the reaction

  • work by lowering the activation required for a reaction to begin

activation energy (Ea)

• the initial input of energy needed to start a chemical reaction

  • even exergonic reactions require an energy “push” to get started

  • enzymes reduce Ea = make it easier for the reaction to proceed @ normal cellular temps

how enzymes work (substrate + active site)

• substrate: the specific reactant an enzyme acts upon

• active site: the clef/groove on the enzyme where the substrate binds + the chemical reaction is catalyzed

process:

1. substrate binds to enzyme’s active site

2. enzyme -substrate complex forms

3. enzyme catalyzes the reaction —> forms enzyme-product complex

4. products are released + enzyme is unchanged, ready to catalyze again

induced fit model

• the enzyme changes shape slightly after the substrate binds

  • this change enhances the fit between the enzyme and substrate

  • facilitates breaking OR forming bonds

why are redox reactions important?

essential to metabolism because they transfer energy through the movement of electrons

OIL RIG

• oxidation is losing (electrons or H)

  • oxidation agent: electron acceptor (gains electron and becomes reduced)

• reduction is gaining (electrons or H)

  • reducing agent: electron donor (loses electron and becomes oxidized)

these reactions are PAIRED, so if one molecule is oxidized, another must be reduced!

redox reactions + making/breaking bonds

• making bonds = storing energy

• breaking bonds = releasing energy

connection to this + redox reactions…

• moving electrons = moving energy

• electron transfers are how cells extract energy from molecules like glucose

  • energy is eventually used to make ATP

electron carriers (NAD+ and FAD)

• electrons are transferred w/hydrogen atoms (H+ or e-)

  • NAD⁺ (oxidized) —> NADH (reduced)

  • FAD (oxidized) —> FADH₂ (reduced)

• these molecules temporarily store energy during redox reactions + later donate it to make ATP

challenges in electron transfer (2)

1. electrons are not easily removed from stable covalent bonds

2. cells use intermediate carriers to safely transfer electrons step by step (ex. cellular respiration

summary (define redox, oxidation, reduction, purpose of electron carriers)

• redox reactions: coupled electron transfers; form foundation for processes like photosynthesis + cellular respiration

• oxidation: loss of electrons or H

• reduction: gain of electrons or H

• electron carriers: vital to store and move energy in metabolic pathways