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Lecture notes for proteins and amino acids
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Chem 145: Biochemistry I Notes I. Amino Acids
Cysteine C Threonine T Tyrosine Y
Glutamic Acid E
Basic Histidine H
Lysine K
Arginine R
pKa (Cα) = ~2. pKa (Nα) = ~9. Essential Amino Acids PVT TIM HALL -Phenylalanine -Valine -Threonine -Tryptophan -Isoleucine -Methionine -Histidine -Alanine -Leucine -Lysine As a human grows into adulthood, the number of essential AA’s become 8 [1] (^) - https://en.wikipedia.org/wiki/Schiff_base#Biochemistry [2] (^) - https://biochemistryquestions.wordpress.com/2008/10/09/supersecondary-structures-motifs-and- Note: Tyrosine is not essential because: P [ O ] ↔
A drug will be soluble in a certain pH if the ration [A-]/[HA] is > 1 therefore, [A-] > [HA]
3. Reactions of Amino Acids Carboxyl groups are formed from amides and esters Amino groups are from Schiff bases* and amides Side chains show unique reactivities: o Cys residues can form disulfides o Few rxns are specific to a single kind of side chain *Schiff bases Lysine is usually involved in forming a Schiff base Schiff base - common enzymatic intermediates where an amine, such as the terminal group of a lysine residue reversibly reacts with an aldehyde or ketone of a cofactor or substrate [1] Application: The common enzyme cofactor PLP forms a Schiff base with a lysine residue and is transaldiminated to the substrate(s). Similarly, the cofactor retinal forms a Schiff base in rhodopsins, including human rhodopsin (via Lysine 296), which is key in the photoreception mechanism 4. Test for presence of Amino Acids Ninhydrin (purple = present) except for proline which gives a yellow color 5. Stereochemistry of Amino Acids All but glycine are chiral (Gly = 2 H’s) L- amino acids predominate in nature [D,L] – nomenclature based on glyceraldehyde where D- = CW and L-CCW [R,S] – absolute configuration; superior to [D,L] (Ile and Leu are named unambiguously in the latter; they have 2 chiral centers) -D and L molecules enantiomers (mirror images) they are diastereomers if they are not mirror images due to the presence of multiple chiral centers [R,S] absolute configuration - Kahn-Ingold-Prelog system o Priority = highest atomic number o H is usually away from you - R-R = S-S (enantiomers) - R,S = S,R (enantiomers) - R-R = S,R (diastereomers) - S-S = R,S (diastereomers) 6. Spectroscopic Properties All amino acids are IR-active due to the presence of their functional groups Only aromatic AA’s are UV active - aromatic – stability, 2n +1, generally insoluble, sp^2 hybridized – planar AA’s absorb at 250-280 nm NMR gives spatial connectivity – structural elucidation Frequency of occurrence (least W and M) Techniques in the Separation of AA 1. Ion-exchange (cation- & anion- exchange) Cation exchange: mixture A , B ,C → a^ salt so l ' n usually NaCl → Na+ b b c c a elutes first and is replaced by Na+^ or the cation of the salt because it has the least affinity for the column (least positive) [1] (^) - https://en.wikipedia.org/wiki/Schiff_base#Biochemistry [2] (^) - https://biochemistryquestions.wordpress.com/2008/10/09/supersecondary-structures-motifs-and-
examples:
Peptide planes contain the peptide bonds Length:
> = > ≡ Partial double bonds are longer than double bonds C=O and C=N; N is bigger than O so C=O Steric combinations on psi and phi Phi = 0o, Psi= 180o Phi = 180o, Psi=0o Phi= 0o, Psi= 0o Helix Handedness eg. Tropocollagen – 3 left-handed helices coiled to form a right-handed triple helix Classes of Secondary Structures:
Alpha helix
Other helices
Beta sheets (compound of beta strands)
Tight turns (beta turns/beta bends)
Beta bulge Beta sheet – loose alpha helix Note: side chains are protruding outwards of a helix (generally hydrophilic interaction with solvent) Interaction among side chains may affect stability. H-bonds must form in order to form the structure. We need at least 8 residues to form an alpha-helix. Amino Acid helix breakers GLYCINE AND PROLINE - destabilize the helix Gly – too flexible due to its small nature Pro – rigidity due to the ring Alpha helix – intramolecular H-bonding Beta sheet – intermolecular H-bonding [1] (^) - https://en.wikipedia.org/wiki/Schiff_base#Biochemistry [2] (^) - https://biochemistryquestions.wordpress.com/2008/10/09/supersecondary-structures-motifs-and-
In beta sheets, side chains alternate between cavities Stability of beta sheets: side chains must fit within the cavities in order to have a stable stacking of beta sheets (a) Parallel beta sheet – both N to C terminal -more extensible because the H- bonds are compacted/folded (same with alpha helix and beta helix) (b) Antiparallel – 1 is C to N, other is N to C -more stable than parallel beta sheet because H-bonding is linear Pitch – distance between 2 turns of a helix Pitch = (#residues/turn)(rise) Regular alpha-helix = 3.6 13 3.6 = #residues per turn 13 = # of atoms in an H-bonded loop Note! (1) H-bonded loop dictates the width of the loop (2) 310 is the thinnest and longest with a rise of 0.20 (assuming that the proteins in comparison have the same number of residues) (3) Turns – at least 4 residues to form a turn (4) Bulge – results from a missed H- bonding Supersecondary structures
- building blocks of domains
Protein Techniques
