Thermodynamics, Chemical reactions and Enzymes

I. Thermodynamics

A. Definition and Overview

B. First Law

• definition: "energy can be changed from one form to another, but it cannot be created or destroyed"
• example
• E _(exhaust) + E _(friction) + E _(movement) = E _(total) or "H" or enthalpy
• E _(reactants) = E _(products) + E _(released)

C. Second Law

• entropy or "S"

http://wps.prenhall.com/wps/media/objects/602/616516/Media_Assets/Chapter17/Text_Images/FG17_03.JPG

• tendency towards randomness or disorder in a system; random molecular movements lead to the conversion of some energy to heat energy
• "all energy transformations are inefficient because every reaction results in increased entropy and loses some useable energy to the surroundings as heat"
• examples: diffusion (leads to increased disorder and release of heat)
• open vs closed systems:

- closed system: isolated with no energy input

Example: "Rat in a box"

-make it an open system: energy input "food, etc." 

-"Time's Arrow": the Universe is a closed system

-difficult to express entropy (S) changes, so new quantity "G" (free energy) is used instead:

∆G = ∆H -T∆S

• re-statement of second law: "in all energy transformations, if no energy leaves or enters the system, the potential energy of the final state will be less than the initial state"

-waterfall

-glucose fire (oxidation) 

• spontaneous and non-spontaneous - not about rate!
• endergonic and exergonic reactions - which is spontaneous?

glucose + oxygen ---> CO₂ + H₂O

CO₂ + H₂O ---> glucose + oxygen

C. Implications of Thermodynamics to Ecosystems

• energy pyramid

http://www.bio.miami.edu/dana/160/pyramid.gif

II. Chemical Reactions and Enzymes

A. Introduction: hydrogen reaction

B. The Energy of Activation

• activated state
• what determines the reaction rate?
• effect of catalyst on activation energy

C. The Role of Enzyme Catalysts

• what are enzymes?
• what do enzymes react with?
• the catalase reaction:

2 H₂O₂ ----> catalase ----> 2 H₂O + O₂

substrate (S) + enzyme (E) ---> enzyme substrate complex (ES) ---> product (P)

• why do enzymes show substrate specificity?
• the Induced Fit Model animation

http://tidepool.st.usm.edu/pix/enzsubstr.gif

• Enzymes have other binding sites in addition to the active site
• cofactors vitamins
• allosteric interaction and feedback inhibition
• sum total of chemical reactions in cells - metabolism
• rate of metabolism regulated (in part) by enzymes
• a series of chemical reactions that produce a particular product is called a metabolic pathway:

A --(1)--> B --(2)--> C --(3)--> D --(4)--> E --(5)--> F --(6)--> G --(7)--> Product

(each step is regulated by a single enzyme; feedback inhibition is an example of of how the synthesis of the product is regulated)

http://scholar.hw.ac.uk/site/biology/topic13.asp?outline=

• competitive and non-competitive inhibition animation

D. Energy in Biological Systems: The Coupled Reaction

• how do non-spontaneous reactions proceed in cells?
• ATP
• the coupled reaction:

For example, in the reaction catalyzed by the Glycolysis enzyme Hexokinase, the two half-reactions are:

• ATP + H₂O <--> ADP + P_i .................. ∆G^o' = -31 kJoules/mol
• P_i + glucose <--> glucose-6-P + H₂O ... ∆G^o' = +14 kJoules/mol

Coupled reaction: ATP + glucose <--> ADP + glucose-6-P .. ∆G^o' = -17 kJoules/mol