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the 6 atoms that comprise biological molecules
HCNOPS
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Electrophiles & their electronegativity values
Have lower electronegativities & always have a formal charge of 0
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Nucleophiles & their electronegativity values
- N: 3.05
- O: 3.44
- S: 2.55 (groomed nucleophile)
Tend to have higher electronegativities
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atoms that form PURE covalent bonds
electrophilic-electrophilic (C-H, C-C)
(C-S is also a pure covalent bond.)
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Bonds between these atoms are never found in living systems.
nucleophilic-nucleophilic
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atoms that form POLAR covalent bonds
- nucleophilic-electrophilic
- (C-O, C-N, O-P, O-H, N-H)
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Priority in biological atoms in determining stereoisomerism
The higher the atomic #, the higher the priority: S > P > O > N > C > H (See slide #4 & 5)
In amino acids, NH3+ will always have 1st priority. 2nd is usually COO- & 3rd is the R group.
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S = L (counterclockwise) & D = R (clockwise) in all amino acids except
Cysteine (has a C-S in the side chain which makes it a higher priority than COO-)
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How many amino acids have only 1 chiral center? How many stereoisomers are possible with 1 chiral center?
17 amino acids
2^1 = 2 stereoisomers
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How many amino acids have 2 chiral centers? How many stereoisomers are possible with 2 chiral centers?
2 amino acids: I (Isoleucine) & T (Threonine)
See slide #7
2^2 = 4 stereoisomers
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How many amino acids have 0 chiral centers? How many stereoisomers are possible with 0 chiral centers?
1 amino acid: G (Glycine) - has 2 H’s bonded to the alpha carbon
See slide #8
2^0 = 1 stereoisomer
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how to calculate possible # of stereoisomers
2^n where n = # of chiral centers
Ex. 1 chiral center would create 2^1 = 2 possible stereoisomers. 2 chiral centers would create 2^2 = 4 possible stereoisomers. 0 chiral centers would create 2^0 = 1 possible stereoisomer
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Hydrophobic amino acids
GAV LIM FWP
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Aliphatic amino acids
GAV LIMP
(Non-aromatic hydrophobic)
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Hydrophobic aromatic amino acids
F (Phenylalanine) & W (Tryptophan)
Has heterocyclic unsaturated rings. See slide #8
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Hydrophilic amino acids
CDESTY HKR NQ
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Amino acids with an ionizable side chain
CDESTY HKR
(All hydrophilic amino acids except N, Asparagine & Q, Glutamine)
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Amino acids with side chains that can engage in H bonding
DESTY HKR NQ
(all hydrophilic amino acids except C, which has an SH in the side chain)
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How is bond type determined?
Difference in electronegativity of the 2 bonded atoms
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What is a hydrogen bond?
Attraction between a nucleophilic (N or O) & electrophilic (H) atom. Not a bond but rather a weak favorable electrostatic force between 2 atoms
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What atoms are required to create a hydrogen bond in biological systems?
Electronegative atom requirement: Nitrogen (3.05) & Oxygen (3.44)
Electropositive atom requirement: Hydrogen (2.20)
NH & OH bonds are very polar
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how to find the # of hydrogen bond donors
Count how many H’s are bonded to N or O
(See slide #14)
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how to find the # of hydrogen bond acceptors
Count how many lone pairs are bonded to N or O
(See slide #14)
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Amino acids whose side chains exhibit resonance
WHYFRED (Tryptophan, Histidine, Tyrosine, Phenylalanine, Arginine, Glutamate, Aspartate)
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Aromatic amino acids
FWHY (Phenylalanine, Tryptophan, Histidine, Tyrosine)
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At a pH of 7.40, which amino acid is able to function ONLY as a H bond donor?
K (Lysine)
(has side chain with NH3+ so 3 H bond donors)
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At a pH of 7.40, which amino acids are able to function ONLY as H bond acceptors?
D (Aspartate) & E (Glutamate)
(has side chains with COO- which have 5 lone pairs so 5 H bond acceptors)
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At a pH of 7.40, which amino acid has the ability to donate one H bond & accept one H bond?
H (Histidine)
(has one H & one lone pair in side chain)
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Calculate the # of stereoisomers for the peptide H3N+ - LQKGT - COO-
(5 amino acids) - (1 G) + (1 more chiral center for T) = 5 chiral centers.
2^5 = 32 stereoisomers
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