ABI 102: Animal Biochemistry & Metabolism

Lecture 01: Chemistry of Life

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Most Abundant Elements in Humans

CHNOPS

Carbon

• 4 ve-

• 4 covalent bonds per atom

• 109.5 degree bond angles

• can form single/double/triple bonds

• bond to many atoms, common to HNOPS

Polymers and Monomers

POLY: Protein (polypeptide) / Nucleic acid (polynucleotide) / Polysaccharide (complex carbohydrate)

MONO: Amino acid / Nucleotide / Monosaccharide (simple carbohydrate)

Cellular Compartmentalization

• way to make molecules for specific purposes

• prevents other molecules in the environment from interacting

• allows for increased concentrations locally

• increase in conc. = increase in rxn

• increased efficiency

• compartment conditions might benefit reaction (pH, available ions, etc.)

• costs energy, time, and substrates to make compartments

Lecture 02: Thermodynamics

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Thermodynamics

study of the rlx among various forms of energy and how energy affects matter

• more macroscopic, thus deals with amounts of matter large enough that avg. properties (temp, pressure) are well defined

Application of Thermodynamics

• used in native folding comformation of proteins

• metabolic pathway design

• why molecules cross mebranes

• how muscles generate mechanical force

  • would like to know if given conditions, will the process be spontaneous?

System

what we’re interested in (organism/rxn vessel)

Surroundings

everything else (rest of universe)

Matter/Energy vs System Chart

Exchange with Surroundings + Type of System

Open:

• matter: YES

• energy: YES

Closed:

• matter: NO

• energy: YES

Isolated

• matter: NO

• energy: NO

Living Organisms

• open systems

  • 1. take in nutrients

  • 2. release waste

  • 3. generate work/heat

Thermo Units & Constants

Energy:

• 1 J = 1Nm = 1CV

• W (work) = F (force) * d (distance) = kgm²/s²

• 1 cal = 4.184 J

• 1 Cal = 1000 cal = 4184 J

Avogadro’s Number = 6.022e23 molecules/mol

Temperature = 273.15 K = 0 degrees C

Boltzmann Constant = k_B = 1.3807e-23 J/K

Gas Constant = R = N_Ak_B , R = 1.9872 cal/Kmol = 8.3145 J/Kmol

First Law of Thermodynamics

Energy can’t be created nor destroyed

• ΔE = Ef - Ei

• ΔE = q + w

  • q = heat absorbed by the system from surroundings

  • w = work done on the system from surroundings

System & Heat

Exothermic = system releases heat = -q

Endothermic = system gains heat = +q

Work done on the system = +w

Work done by the system = -w

Enthalpy

heat released or taken in at constant pressure

• Work can be divided into 2 categories

• -PΔV = pressure-volume work (expansion)

• w’ = all other work

w = -PΔV + w’

• ΔE = Ef - Ei = q+w

• ΔH = ΔE + PΔV

• ΔH = q + w + PΔV

• ΔH = q_p + (-PΔV + w’) + PΔV

• ΔH = q_p + w’ (w’ = 0)

• ΔH = q_p

Hess’s Law

• regardless of the multiple stages or steps of a rxn, ΔH = sum off all changes

• enthalpy = state function; depends only upon state of system and NOT the way in which the system acquired the state

Second Law of Thermodynamics

• spontaneous processes occur in directions that increase disorder of the universe

• entropy = measure of the number of specific ways in which a thermodynamic system can be arranged (disorder)

  • S = k_B lnW

    • k_B = Boltzmann’s constant

    • W = # ways to arrange system

Entropy

for any constant processes (ΔE = 0), a spontaneous process is characterized by ΔS > 0

• any spontaneous process MUST cause the entropy of. the universe to increase

  • ΔS_system + ΔS_surroundings = ΔS_universe > 0

  • ΔS >= q_p/T

    • entropy change of a reversible process at a constant temperature can be determined straightfowardly from the measurements of heat transferred (and temperature maintained)

Gibbs Free Energy

the change in energy for a process that combines enthalpy, entropy, and temperature (assuming constant pressure)

• ΔG < 0 spontaneous (exergonic)

• ΔG = 0 at equilibrium

• ΔG > 0 not spontaneous (endergonic)

Enthalpy & Entropy Table

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Entropy (cont)

Entropy is a function of concentration

• free energy change of chem rxn depends on the concentrations of both its reacting substances (reactants) and its reaction products

• thus, the concentrations of reactants and products are important; oftentimes the availability of reactants dictates rxn direction