Bio lesson 7

thermodynamics

energy changes

kinetic energy

energy of motion

potential energy

stored energy

redox reactions

-oxidation: atom loses an electron

-reduction: atom gains an electron

-paired as redox reactions

-in diagram, molecule a is oxidized bc electron is transferred from A to B

-molecule A becomes pos charged while B becomes neg charged

first law of thermodynamics

-energy cant be created or destroyed

1. can only change from one form to another

2. some energy is lost as heat (kinetic) during energy conversion

3. total amt of energy in universe is constant

-energy continuously flows through biological world from Sun to heat

second law of thermodynamics

-entropy/disorder is continuously increasing

-energy transformations proceed spontaneously to convert matter from a more odered/less stable form to a less ordered/more stable form

-disorder happens spontaneously in that the room will become more disorganized over time, in order to reestablish organization, there must be an energy input so that the room may return to an ordered state (room ex)

gibbs free energy equation

delta G= change in free energy

H= enthalpy

T= temp

S= entropy

-can predict whether or not a reaction is spontaneous

pos deltaG reactions

-require energy to proceed

-products have more free energy than reactants, ie products have higher H or lower S (or both)

-not spontaneous bc they require energy input (endergonic)

neg deltaG reactions

-occur spontaneously

-prod have less free energy than reactants ie prod have lower H of higher S (or both)

-release energy, so spontaneous (exergonic)

-not necessarily instantaneous (still require energy input to start)

activation energy

-extra energy required to initiate chem reaction

-destabilize existing bonds

-an exergonic reaction’s rate depends on the activation energy required

1. larger activation energy= slower reaction rate

-to increase reaction rate…

1. inc energy of reacting molecules (heating)

2. or use catalyst to lower activation energy (since biological systems are functional only in a limited temp range, cells need catalysts to inc reaction rates)

catalysts

-substances that influence chem bonds in a way that lowers activation energy of a reaction

-cannot violate laws of thermodynamics

1. can’t make an endergonic reaction spontaneous

-can’t alter the proportion of reactant turned into product

exergonic reactions need activation energy

the activation energy of catalyzed reaction is significantly lower than that of the uncatalyzed reaction. thus, less energy is required to initiate the catalyzed reaction

enzymes as biological catalysts

-most enzymes are proteins and store RNA molecules act as enzymes

-have unique 3D shapes that stabilize transient association btwn substrates

-enzyme not unchanged/consumed in reaction and can therefore be reused

1. diff cells have diff enzymes. enzymes specify call structure/function

-enzymes may be soluble/associated with membranes (function in the soluble material that makes

the active site

-a pocket or cleft for substrate binding

-allows precise fit of substrate

-applies stress to distort bond(s) to lower activation energy

-enzymes may change shape to maximize contact w/ substrate (induced fit)

enzyme cycle

1. substrate (sucrose) is made of glucose and fructose bonded together

2. the substrate binds to the active site of the enzyme, forming enzyme-substrate complex

3. the binding of substrate and enzyme places stress on glucose-fructose bond, which then breaks

4. prod are released and enzyme is free to bind w/ other substrates

factors that influence enzyme function

-concentration of substrate

-concentration of enzyme

-any chem/phys condition that affects the enzyme structure

1. temp

2. pH

3. regulatory molecules

enzyme regulatory molecules

-allows cells to control enzyme activities (for allosteric enzymes)

-one way that cells regulate the activity of allosteric enzymes is through enzyme inhibitors

inhibitors

-molecule that bind to and decrease the activity of an enzyme

-competitive/non competitive

competitive inhibitor

competes with substrate for active site

non competitve

binds to enzyme at a site (allosteric site) other than active site. causes shape change that makes enzyme unable to bind substrate

metabolism

-total of all chem reactions carried out by organism

-anabolic reactions (anabolism) expend energy to synthesize molecules, ex: amino acids, fatty acids

-catabolic reactions (catabolism) harvest energy by the breakdown of molecules

biochemical pathway

-many chem reactions in the cell are organized into biochem pathways

-in these paths, reactions occur in a sequence so that the product of one reaction is the substrate for the next reaction

-many steps may occur within organelle or a certain membrane. ex: the inner membrane of the mitochondria is essential for the ability of eukaryotic cells to synthesize ATP

feedback inhibition

-cells use to control many biochemical pathways

-end prod of pathway binds allosteric site on first enzyme in pathway

-a control mechanism that shuts off biochemical pathway so raw materials/energy aren’t wasted when sufficient amts of of end products are prod

-therefore, only necessary end prod is maintained

-no feedback inhibition pathway continues to make end prod regardless of whether or not sufficient prod already exists

ATP

-2 high energy bonds btwn phosphate groups are key to energy storage. stores energy in the covalent bonds of the phosphate groups

-these bonds are unstable, easily broken by hydrolysis, releasing energy used to drive endergonic reactions

-in most reactions, only outermost bond hydrolyzes prod. ADP and Pi

-in some reactions, the terminal phosphate group of ADP, may also be hydrolyzed prod. AMP and Pi

-ATP not suitable for long term energy storage (fats+ carbs are better)

the ATP cycle

-high turnover rate in cells. ATP is constantly synthesized and used (cells store only a few seconds worth of ATP)

-ATP hydrolysis is used by cells to drive endergonic reactions. often done in coupled reactions, where an exergonic reaction (ATP hydrolysis) is combined w/ endergonic reaction, leads to overall net neg. deltaG

-ATP synthesis depends on energy from exergonic cellular reactions

-ATP hydrolysis provides energy for endergonic cellular processes

-prod. of ATP hydrolysis are ADP and inorganic phosphate. they then serve as the reactants for the synthesis of new ATP

phosphorylation

-ATP is used to control the activity of many proteins through reversible process of phosphorylation/dephosphorylation. functions like a molecular light switch

-in order to switch the protein into the active/on state, enzyme kinase binds and hydrolyzes ATP, and covalently attaches the released phosphate group to a target protein

-in order to switch the protein from on to off, enzyme phosphatase removes the phosphate group from the relevant amino acid side chain

-reg of target proteins depends on opposing actions of kinase and phosphatase