lecture 02 - 1 sep 2010 - thermo

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Thermodynamics

BIOCHEM 227 SUMMER 2010

Lecture 2

Wednesday, September 1, 2010

TODAY

Continue: example from last lecture

Chemical elements in biochemistry

Review of functional groups

Review of basic thermodynamics

BCH 227 FALL 2010 LECTURE 2: THERMODYNAMICS 1 SEP 2010


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An Example: Enzyme Design

Nature 453: 190 (2008)



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Enzyme Design Example

Design an enzyme to carry out the Kempelimination

abstract a proton via a general base

no natural enzyme for this reaction

How? Asp or Glu sidechain

His positioned by Asp



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Design parameters

structure: catalytic residues, other residues

pKa

quantum calculations

need a protein scaffold

Result: functional catalysts for both designs

Activity confirmed by assays

Structure confirmed by crystallography




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Comparison of design (grey) and actual (cyan):




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Implication: possibility of designing customcatalysts

pharmaceuticals

energy

chemical industry etc

Chemical Elements andFunctional Groups



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Chemical Composition

~300026Macromolecules (proteins, nucleicacids, and polysaccharides)

~3000.2Other small molecules

501Fatty acids and precursors

1000.4Nucleotides and precursors

1000.4Amino acids and precursors

2501Sugars and precursors

201Inorganic ions

170Water

NUMBER OF TYPES OFEACH MOLECULE

PERCENT OFTOTAL CELL

WEIGHT

Constituent

Chemical Composition



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Chemical Composition Chemical Composition



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Review of Thermodynamics

Thermodynamics

Why are we concerned with thermo?

What can it tell us?



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Life: Not in Equilibrium!



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Equilibrium Constants

[products]

[reactants]eqK =

at equilibrium

Reaction Quotient

[products]

[reactants]

Q =

not at equilibrium



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Le Chteliers Principle

If a reaction at equilibrium is subjected to achange in conditions that displaces it fromequilibrium, it adjusts to a new equilibrium.

Free Energy

STHG =



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Free Energy

lnG G RT Q = +

lnG G RT Q = +



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lnG G RT Q = +

( ln )ln

G G RT Q dQG Q RTQ RTQ Q C

= += + +

Free Energy

ln eqG RT K =



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Activation Energy & Catalysis Activation Energy & Catalysis



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Arrhenius Equation

aE

RTk Ae

=

where, from transition-state theory:

A = kbT/h

Ea = G

Coupling of Processes



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THINGS TO KNOW

Be familiar with which elements have roles inbiology, roughly what those roles are and why

Be familiar with functional groups found inbiological molecules

Thermo Understand basic thermo discussed today

(We will revisit the enzyme design paper)


lecture 02 - 1 sep 2010 - thermo

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