the energy of life

• the cell is a miniature chemical factory where reactions occur

• cellular respiration extracts energy stored in sugars and other fuels

• cells apply this energy to perform work

• some organisms convert energy to light - bioluminescence

metabolism transforms matter and energy

• metabolism is the totality of an organism’s chemical reactions

• it is an emergent property of life that arises from orderly interactions between molecules

• not a physical reaction nor random

• because viruses can’t metabolize, they are not alive

metabolic pathways

• metabolic pathways - begins with a specific molecule and ends with a product

• each step is catalyzed by a specific enzyme

  • each enzyme only works for that specific molecule and reactions - no enzyme can perform all the reactions in the metabolic pathway

• each reaction is fueled by the reaction before it so it must go through all the reactions to reach the final product

• catabolic pathways release energy by breaking down complex molecules

  • cellular respiration, the breakdown of glucose is catabolic

• anabolic pathways consume energy to build complex molecules from simpler ones

• bioenergetics is the study of how energy flows through living organisms

forms of energy

• energy is the capacity to cause change

• exists in various forms, some of which can perform work

• kinetic energy - energy associated with motion

• thermal energy - kinetic energy associated with random movement of atoms or molecules

  • heat - thermal energy in transfer between objects

• potential energy - energy that matter possesses because of its location or structure

• chemical energy - potential energy available for release in a chemical reaction

• energy can be converted from one form to another

  • our bodies maintain heat because heat is a byproduct of energy conversion

laws of energy transformation

• thermodynamics - the study of energy transformations

• an isolated system is unable to exchange energy or matter with its surroundings (eg. thermos)

• in an open system, energy and matter can be transferred

• organism are open systems

laws of thermodynamics

1. energy can be transferred and transformed but it cannot be created no destroyed (principle of conservation of energy)

2. every energy transfer or transformation increases the entropy of the universe

   1. entropy - measure of molecular disorder or randomness

   2. during every energy transfer or transformation, some energy is unusable and is often lost as heat

• living cells convert organized forms of energy to heat, a more disordered form of energy

• spontaneous processes - occur without energy input

  • increases the entropy of the universe

  • releases energy -- catabolic process

• nonspontaneous processes - will only occur if energy is provided

  • decreases entropy

  • absorbs energy to create order -- anabolic process

biological order and disorder

• organisms create ordered structures from less organized forms of energy and matter

• organisms also replace ordered from of matter and energy with less ordered forms

  • eg. animals consume complex molecules in food and release smaller, lower energy molecules and heat (catabolic)

  • cellular respiration is a catabolic reaction as it is the breaking down of glucose (order → disorder)

  • photosynthesis is an anabolic reaction since it converts energy into glucose (disorder → order)

• the evolution of more complex organisms does not violate the second law of thermodynamics

  • entropy (disorder) may decrease in a particular system (photosynthesis) but the total entropy of the system and surroundings increases

free-energy change

• in order to know which reactions occur spontaneously and which require the input of energy, they need to determine the energy and entropy changes that occur in chemical reactions

• free-energy change ΔG

  • a living system’s free energy is energy that can do work when temperature and pressure are uniform as in a living cell (does not change even with a catalyst)

• the change in ΔG during a process is related to the change in enthalpy

• ΔG is negative for all spontaneous processes

  • spontaneous processes release energy

  • processes with 0 or positive ΔG are never spontaneous

• spontaneous processes can be harnessed to perform work

free energy, stability and equilibrium

• free energy - a measure of a system’s instability, its tendency to change to a more stable state

• during a spontaneous change, free energy decreases and the stability of a system increases

• equilibrium is a state of maximum stability

  • you die if you reach equilibrium

• a process is spontaneous and can perform work only when it is moving towards equilibrium

• more free energy (G) → less stable and greater work capacity

• in a spontaneous change, the free energy of the system decreases (∆G < 0) → the system becomes more stable and the released free energy can be harnessed to do work

• less free energy → more stable and less work capacity

free energy and metabolism

• the concept of free energy can be applied to the chemistry of life’s processes

• exergonic reactions - proceed with a net release of free energy and is spontaneous

  • negative ∆G

  • catabolic reaction

  • as the reaction proceeds, energy is released meaning the free energy of the products is LESS than that of the reactants (∆G = products - reactants)

  • 

• endergonic reactions - absorb free energy from its surroundings and is nonspontaneous

  • positive ∆G

  • anabolic reaction

  • as the reaction proceeds, energy is absorbed from the surroundings meaning the free energy of the products is GREATER than that of the reactants

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equilibrium and metabolism

• reactions in a closed system eventually reach equilibrium and can then do no work

• cells are not in equilibrium -- they are open systems experiencing a constant flow of materials

• a defining feature of life is that metabolism is never at equilibrium

• a catabolic pathway in a cell releases free energy in a series of reactions

ATP powers cellular work

• a cell does three main kinds of work

  • chemical work - pushing endergonic reactions

  • transport work - pumping substances against the direction of spontaneous movement

  • mechanical work - contraction of muscle cells

• to do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

• most energy coupling in cells is mediated by ATP

the structure and hydrolysis of ATP

• ATP (adenosine triphosphate) is the cell’s energy shuttle

• it is composed of ribose (sugar), adenine (nitrogenous base), and 3 phosphate groups

• cellular respiration exists to form ATP

  • catabolic and exergonic since it breaks down glucose

• the bonds between the phosphate groups of ATP’s tail can be broken down by hydrolysis

• energy is released when the terminal phosphate bond is broken

• this release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

how the hydrolysis of ATP performs work

• the 3 types of cellular work are powered by the hydrolysis of ATP

• in the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

• the coupled reactions are exergonic overall since there is left over energy bc they are not perfectly efficient

• ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule

• the recipient molecule is now a phosphorylated intermediate

  • phosphorylated - means phosphorus is added to it

• transport and mechanical work in the cell are also powered by ATP hydrolysis

• ATP hydrolysis leads to a change in protein shape and binding ability

• active transport - requires energy

  • can go against the concentration gradient

  • transports proteins that are too large

• passive transport - does not require energy

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the regeneration of ATP

• ATP is a renewable resource that is regenerated by the addition of a phosphate group to adenosine diphosphate (ADP)

• the energy to phosphorylated ADP comes from catabolic reactions in the cell

  • ADP + phosphorus = anabolic

• the ATP cycle is a revolving door through which energy passes during its transfer from catabolic and anabolic pathways

  • using ATP in cellular respiration is catabolic because it breaks down into ADP and the phosphorylated intermediate

enzymes speed up metabolic reactions

• a catalyst is a chemical agent that speeds up a reaction without being consumed by it

• an enzyme is a catalytic protein

  • eg. sucrase is an enzyme that catalyzes the hydrolysis of sucrose

  • needs energy 99% of the time to work

• every chemical reaction between molecules involves bond breaking and bond forming

• the initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (Eₐ)

• activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings

• because ∆G is negative, it is an exergonic reaction

• the bump in the graph is the activation energy

  • catalysts reduce the EA

• enzymes do not change ∆G because if it does, it is taking part in the reaction

• in catalysis, enzymes or other catalysts speed up specific reactions by lowering the EA barrier

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substrate specificity of enzymes

• the reactant that an enzyme acts on is called the enzyme’s substrate

• enzyme puts pressure on the bonds within the substrate to break it down into different sections

• energy released from breakdown is ∆G

• the enzyme binds to its substrate, forming an enzyme-substrate complex

• while bound, the activity of the enzyme converts substrate to product

• the reaction catalyzed by each enzyme is very specific

• the active site is the region on the enzyme where the substrate binds

• induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

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• in an enzymatic reaction, the substrate binds to the active site of the enzyme

• enzymes are extremely fast acting and emerge from the reactions in their original form

• in the long term, structure doesn't change

• very small amounts of enzymes can have huge metabolic effects because they are used repeatedly in catalytic cycles

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• in prokaryotes, if half of the substrate is rare and the other is abundant, the full substrate cannot be made

• the active site can lower an EA barrier by:

  • orienting substrates correctly

  • straining substrate bonds

  • providing favorable microenvironments

  • covalently bonding to the substrate

• the rate of an enzyme-catalyzed reaction can be sped up by increasing substrate concentrations

• when all enzyme molecules have their active sites engages, the enzyme is saturated

• if the enzyme is saturated, the reaction rate can only be sped up by adding more enzymes

effects of local conditions on enzymes

• an enzyme’s activity can be affected by

  • general environmental factors such as temp and PH

  • chemicals that specifically influence the enzyme

  • levels of enzyme activity will change

• each enzyme has an optimal temperature in which it can function or else it will be denatured

• each enzyme has an optimal pH in which it can function

  • this is why our bodies have buffers

• optimal conditions favor the most active shape for the enzyme molecule

cofactors

• cofactors - non-protein enzyme helpers

• may be inorganic (like a metal) or organic

• an organic cofactor is called a coenzyme

  • eg. vitamins

• they attach in the passive site (allosteric site) to help shape enzymes for certain substrates

  • active site - where the substrate goes

  • allosteric site - where the coenzyme goes

inhibitors

• competitive inhibitors - bind to the active site of an enzyme, competing with the substrate

  • has the same shape as the substrate to inhibit the proper substrate from binding to the enzyme

• non-competitive inhibitors - bind to the passive site of the enzyme causing the enzyme to change shape and make the active site less effective

• eg. toxins, poison, pesticides, antibodies

• like how tiktok inhibits people from doing work

• opposite of inhibitor is activator

• when the effects on an inhibitor can be reversed by adding more substrate, it is a reversible inhibitor

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the evolution of enzymes

• enzymes are proteins encoded by genes

• changes in genes lead to changes in amino acid composition of an enzyme

• altered amino acids, particularly at the active site, can result in novel enzyme activity or altered substrate specificity

• under environmental conditions where the new function is beneficial, natural selection would favor the mutated allele

regulation of enzyme activity

• chemical chaos would result if a cell’s metabolic pathways were not tightly regulated

• a cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes

allosteric regulations

• allosteric regulation may either inhibit or stimulate an enzyme’s activity

• allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

• most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site

• the enzyme complex has active and inactive forms

• the binding of an activator stabilizes the active form of the enzyme

• the binding of an inhibitor stabilizes the inactive form of the enzyme

  • eg. some drugs inhibit enzymes from doing its job

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• cooperativity - a form of allosteric regulation that can amplify enzyme activity

• one substrate molecule primes an enzyme to act on additional substrate molecules more readily

• cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site

• in feedback inhibition, the end product of a metabolic pathway shuts down the pathway

  • prevents a cell from wasting chemical resources by synthesizing more product than needed

  • eg. a thermostat tells the furnace when to stop once the temperature is high or low enough

• negative inhibition is good for the body

• positive inhibition ONLY occurs during pregnancy

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• only happens when the product is in excess otherwise, it will get used up

localization of enzymes within the cell

• structures within the cell help bring order to metabolic pathways

• some enzymes act as structural components of membranes

• in eukaryotic cells, some enzymes reside in specific organelles

  • eg. enzymes for cellular respiration are located in mitochondria