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Biol 201 Exam 1 Notes:
Unit 1: Aqueous Ionization Tendencies:
Noncovalent interactions: Ionic>Ion-PD>H-bonding>PD-PD>ID-PD>ID-ID
Predominant Species (PS): the molecule that represents the majority
Average Molecule (AM): represents the fractional charges of each functional group at a given
pH
- AM is more precise and accurate than PS
Zwitterion: has separate positive and negative charged groups; occurs at the pH range where
ionization of one functional group begins and the other has ended; whole molecule is neutral;
occurs at the pI
Buffers: aqueous systems that resist change in pH when small amounts of acid or base are
added; contains weak acid and conjugate base; flat zone on titration curve 1 unit below and
above pKa

- Explained by Henderson-Hasselbach equation:
- Macromolecules with weak acid/base functional groups can act as buffers in the cell
Ionization Tendencies of Functional Groups:
Anionic Groups:
1
...
Carboxyl→Carboxylate (COOH → COO-)
3
...
Phosphoryl→Phosphate
5
...
Amino→Ammonium (R-NH2 → R-NH3+)

2
...
Pyrrolidine→Pyrrolidinium

4
...
Amido

2
...
9

Charge at pH 8
...
7

alpha-COOH: pKa 1
...
5

-1

-1

R-SH: pKa 8
...
5

-1

alpha-NH3+: pKa 10
...
5

Total Charge

+0
...
5

-1
...
1

Unit 2A: Globular Protein Structure
Amino acids: alpha carbon is chiral; only L/S enantiomer is incorporated in proteins
Amino acyl residue: amino acid incorporated in a protein; its functional groups may have
different pKa’s than amino acids
- Average mass of amino acyl residues: 110 Da; average mass of amino acids: 128 Da
Monomeric proteins: one subunit
Oligomeric proteins: multiple subunits
Protomer: indentical subunits of an oligomeric protein
Domain: Part of one whole polypeptide chain; usually serves a specific function; independently
stable and undergoes movements as single entity
Oligopeptide: a few (20-50) amino acids joined by peptide bonds
Polypeptide: many (>50) amino acids joined by peptide bonds

Peptide Bonds:

-

Bonds are planar due to resonance and double-bond character, which makes it more
rigid; prevents the N in the peptide bond from being an H-bond acceptor since its lone
pair contributes to resonance
- Hydrolysis is exergonic, but very slow due to high activation energy
Hydropathy: rating of hydrophobic or hydrophilic behaviour; measured in hydropathy index or
by measuring the concentrations of a protein in a water phase compared to a nonpolar solvent
phase; hydrophobic and hydrophilic molecules have attractive relationship, but this relationship
is weaker than the ones formed by separating hydrophobic and hydrophilic molecules, and thus
separation is favourable
H-bonds and pH: when functional groups become fully ionized, they no longer participate in Hbonds as a donor or acceptor
Globular Proteins: spherical, somewhat water soluble
Fibrous Proteins: elongated protein, provide structural support
Membrane Proteins: contain hydrophobic domains, associated with membrane permanently or
transiently
Secondary Protein Structure: usually amphipathic, and usually incorporated in membranes
a) Alpha helix: backbone in a right-hand coil; H-bonds between C & N groups 4 amino acids
apart; each turn is 5
...
54nm) long, and incorporates 3
...
5nm
- #H-bonds in helix= #residues – 4
b) Antiparallel Beta-sheet: pleated sheet with lined-up inter-strand hydrogen bonds; Hbonds between adjacent C & N groups; 2 amino acids correspond to 7 angstroms
(0
...
5 angstroms (0
...
g
...
Hydrophobic effect stabilizes proteins
2
...
Adjacent segments in sequence are usually proximal to each other when folded
4
...
3D product and folding process
2
...

Holoenzyme: complete, catalytically active enzyme with bound coenzyme and/or metal ion
Apoenzyme: protein part of holoenzyme
How enzymes catalyze reactions:
1
...
Binding energy between enzyme and substrate contributes to specificity but also can be
used to decrease activation energy
3
...
Ultimately, it speeds up reaction by lowering activation energy
How enzymes overcome thermodynamic barriers:
1
...
Solvation shell of H-bonded water stabilizing molecules in solution: overcome by
forming noncovalent interactions between substrate and enzyme, causing desolvation
3
...
Required proper alignment of catalytic functional groups: binding energy changes
conformation of enzyme when substrate binds, activating the active site
Acid/base catalysis: requires ionizable functional groups; transfer of protons
a) Specific Acid/Base Catalysis: uses only ions in water; usually not strong enough to
stabilize intermediate

b) General Acid/Base Catalysis: weak organic acids/bases supplement water
Covalent catalysis: requires groups with heteroatoms that can act as nucleophiles; transient
covalent bond formed b/w enzyme and substrate; only works when newly formed pathways
have lower activation energy than uncatalyzed pathway
Metal Ion Catalysis: metals form ionic interactions with substrate to orient it for reaction or
stabilize transition states; can do redox reactions by changing metal ion’s oxidation state
Enzyme-Substrate Complex: stability is influenced by same factors that influence folding
stability (breaking solvation layer, hydrophobic effect)
At optimum pH:
- Reaction rate is maximal given [Substrate], [enzyme] and temperature
- pH affects enzyme function with deprotonation and protonation
- Optimal balance of protonated/deprotonated reactive residues



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