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1 Metabolism/ Thermodynamics
Metabolism: totality of an organisms chemical reactions Metabolism is emergent life property, cell interactions with environment
Metabolic Pathways
Metabolic pathway: begins with a specific molecule, which is altered through a series of defines steps resulting in a certain product, each step catalyzed by an enzyme Catabolic pathways: release energy by breaking down complex molecules to simpler, degradative process (cellular respiration) Pathways can have more than one starting molecule Anabolic pathways: consume energy to build complicated molecules from simpler ones, aka biosynthetic pathways (protein from amino acids) Energy released from the downhill reaction of catabolism can be stored and used to drive the uphill reaction of the anabolic pathways Bioenergetics: the study of how organisms manage their energy resources
Forms of Energy
Energy is the capacity to cause change. (Ability to rearrange collection of matter) Kinetic energy: relative motion of objects Heat, thermal energy: kinetic energy associated with random movement of atoms or molecules Potential energy: energy no kinetic, energy that a matter possesses because of location and structure Chemical energy: potential energy available for release in a chemical reaction Diver climbs up releasing food chemical energy, muscle movement causes kinetic energy transformed into potential (increase in height)
During every energy transformation some energy becomes unusable (not able to do work) Heat dissipates into surroundings, heat is associated with random motion of atoms or molecules Increasing entropy in decay of an unmaintained building, or cheetah producing heat Spontaneous: a process that can occur without an input of energy A spontaneous process increases entropy Nonspontaneous: a process that cannot occur on its own, will happen only if energy is added to the system For a process to occur spontaneously, it must increase the entropy of the universe
Equilibrium: state of maximum stability Systems never spontaneously move away from equilibrium Systems at equilibrium can not spontaneously change so they can do no work
Metabolism
Exergonic reaction proceeds with a net release of free energy, G decreases and G is negative (spontaneous) The magnitude of G for exergonic reactions represent the amount of work the reaction can perform Greater the decrease in free energymore amount of work Endergonic reaction absorbs free energy from its surroundings Stores free energy so G increases and G is positive (Nonspontaneous) Cells dies at equilibrium because no reactions G=0 Metabolism as a whole is never at equilibrium Constant flow of materials in and out keeps metabolic pathways from reaching equilibrium, and the cell continues to do work Product of one reaction is a reactant of the next step
The recipient of the phosphate group is the phosphorylated and undergoes a change that performs work Mechanical, transport, and chemical works are almost always powered by hydrolysis of ATP In the synthesis of amino acid glutamine, glutamic acid and ammonia are usedATP phosphorylates glutamic acid making it less stableammonia displaces the phosphate group forming glutamine
Regeneration of ATP
ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP ATP cycle it couples with exergonic processes to the endergonic ones If ATP could not be regenerated by phosphorylation of ADP then humans would use their body weight in ATP each day Regeneration is endergonic, not spontaneous, free energy must be spent Plants use light energy to produce ATP, cellular respiration also has catabolic processes Chemical potential energy is stored in the ATP
Substrate Specificity
Substrate: the reactant an enzyme acts on Enzyme-substrate complex: enzymes bind to its substrates Active site: restricted region of the enzyme that binds to the substrate Induced fit: interactions between the chemical groups on the substrate and enzyme cause it to change shape slightly so it fits more snug
Catalysis in Active Site Substrate held by weak hydrogen and ionic bonds R groups of amino acids on the enzyme catalyze reaction, and product departs Enzymes normally can do both forward and reverse reactions, direction of equilibrium 1. Substrate enters active site, induced fit 2. Held by weak hydrogen or ionic bonds 3. Active site the r groups of amino acids lower EA barrier and speed rate Provides a template for orientation Stressing the substrates and stabilizing the transition state Favorable microenvironment Participating directly in catalytic reaction (may need covalent bond) 4. Substrates are converted into products 5. Products are released 6. Active site is available When enzyme population is saturated, the only way to increase rate is to add more enzymes
Cofactors
Cofactors: non protein helpers fro catalytic activities, can be tightly bound permanent, or bind loosely Coenzyme: when a cofactor is organic molecule
Enzyme Inhibitors
If attaches by covalent bonds it is normally irreversible Bind by weak bonds normally Competitive inhibitors: resemble the normal substrate and compete for admission, they reduce productivity of enzymes by blocking active sites Can be overcome by increasing concentration of the substrate Noncompetitive inhibitors: do not directly compete, impede enzymatic reactions by binding to another part Enzyme will change its shape and the active site will be less effective Toxins and poisons are irreversible Antibiotics are inhibitors of bacterial enzymes