Review Material I

• Chapter 2:

dielectric constant
solubility
pH and buffers including Henderson-Hasselbalch equation

problem set

• Chapter 3:

Knowledge of thermodynamics allows us to determine whether or not a physical property is possible; allows us to understand why molecules fold, how metabolic pathways are designed, etc.

Free Energy: ÆG = ÆH - TÆS

Enthalpy: heat of reaction based on bound energy since pressure and volume are basically constant for biological systems.

Entropy: measure of randomness of system. Generally entropy increases in spontaneous process but not always therefore not good predictor or spontaneity.
negative ÆG = spontaneous reaction positive
ÆG = non-spontaneous reaction

Standard Free Energy Go': free energy under standard conditions (298oC, 1M concentration of reactants, 1 atm, pH 7)
G' = Go' + RTlnK K = the product of the concentrations of product divided by product of reactant concentrations.
At equilibrium, G = 0 and therefore K = Keq. Keq = -ÆGo/RT

Coupled Reactions: a spontaneous reaction can drive a non-spontaneous reaction. Some examples of high energy molecules include, phosphoenolpyruvate; 1,3 diphosphoglycerate; acetyl-S-CoA; ATP

problem set
 

• Chapter 4:

structure of L- isomer amino acids
side chain classification (aliphatic, OH or S side chain, aromatic, basic or acidic)
ionization constants for functional groups isoelectric point

problem set

• Chapter 5:

Prior to protein purification:
develop an assay
choose source
solubilize
stabilize

Characteristics by which proteins can be separated:
solubility
charge
polarity
size
specificity
combinations of these characteristics can be used in one separation medium
 
problem set
 

• Chapter 6: Four levels of protein organization

Primary structure: amino acid sequence
To determine protein sequence, first purify.  Amino acid composition analysis may provide some structural insights or hydrophobicity or hydrophilicity of protein.  Determination of subunits or disulfide bonds is also necessary.  Amino and carboxy- terminal analysis can be using when aligning sequences from peptide fragments.  Before complete sequencing of the molecule can be accomplished, chemical and enzymatic fragmentation, must occur to break the molecule into managable pieces.  Lastly, align fragments and assign disulfides

Secondary structure: spatial arrangement of peptides in backbone. To determine helix, sheet or secondary structure prediction use Ramachandran plot, CD, or NMR.

Super-secondary structure: typical types include, meander, beta-alpha-beta, Greek key, nucleotide fold, leucine zipper/zinc finger

Tertiary structure: 3-D structure of entire polypeptide. The stabilization forces for this structure include, hydrogen bonds, hydrophobic interactions, ionic interactions, and disulfide bonds

Quaternary structure: spatial arrangement of subunits
 
 

problem set

Back to Biochem I tentative schedule

Contact: Stapleton@wmich.edu

URL- http://www.wmich.edu/pathname/filename.html (if known, otherwise omit) Revised Date: June 24, 1997