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What are the five principal components of the basic chemical structure of a free amino acid:
- 1) Alpha carbon (Cα)
- 2) Alpha carbon hydrogen (H)
- 3) Amino group (NH3+1)
- 4) Carboxylate group (COO-1)
- 5) An R group (also called a side chain, which may or may not be ionizable)
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Proline is an example of a <BLANK> acid why?
Imino acid because it has an +NH2 group instead of an +NH3 group
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What's the structure of an Amino group?
H3N+--R
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What's the structure of an Amine group?
H3N+--R
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What's the structure of an Imino group?
H2N: --R
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Define ionizable (as it pertains to amino acids)
The side chain of the amino acid can lose or gain protons and is dependent on pH
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How many ionizable functional groups does a free amino acid have?
- minimum of 2
- maximum of 3
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Formal Charge Formula
F.C. = Valence e- - (1/2 Bonding e-) + #Lone pair e-
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The 6 atoms that biomolecules consist of
C.H.N.O.P.S.
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Classify each as of the 6 atoms of biomolecules
- CHP: Electrophiles; toggle between +1 & 0; ↓
- EN
- NOS: Nucleophiles, toggle between 0 & -1; ↑
- EN
- *We wont talk about P*
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What is Proline & Draw it
- Proline is one of the 20 protein amino acids but its an Imino acid
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What are the 2 subsets under the hydrophobic class (9 of 20), which amino acids belong to each & what are their defining characteristics?
- 1. Aliphatic [GAV LIM P]: Non cyclical shape; straight chain
- 2. Aromatic [FW]: Cyclic & Unsaturated (has 1 or more double bonds)
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Defining characteristic of hydrophobic aa's
No Oxygens or Nitrogens
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Define Aliphatic (Hydrophobic) & which amino acids belong under this category
GAV LIM P: Non cyclical shape; straight chain2.
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True Aliphatics vs G, M, P Aliphatics
True aliphatics are only made up of Carbons & Hydrogens but G, M, P, have "blemishes"
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Define Aromatic (Hydrophobic) & which amino acids belong under this category
F, W: Cyclic & Unsaturated (has 1 or more double bonds)
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Whats different about Tryptophan aka W
Tryptophan is heterocyclic
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Defining characteristic of hydrophilics
- Overwhelmingly contain Nitrogen & Oxygen & theres lots of H bonding
- N & O are very EN so they cause H bonding
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H bond acceptors are [BLANK]
the lone pairs (Must satisfy the octet rule)
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H bond donors vs H bond acceptors
- # donors = # Hydrogens
- # acceptors = # lone pairs
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How many acceptors & donors does this O have?
1 donor & 2 acceptors
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Hydrogen Bonding, Strict Acceptors
- D (Aspartate) & E (Glutamate)
- 5 Acceptors
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Hydrogen Bonding, Strict Donors
K (Lysine)
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What are 2 characteristics of the Hydrophilic class (11 of 20) & which amino acids belong in each?
- [DESTY HKR NQ] : can Hydrogen bond
- [CDESTY HKR] has an ionzable side chain
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What is a hydrogen bond as it pertains to amino acids?
Its a favorable, weak, electrostatic attractive force between the 2 atoms
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Special characteristic about H & Y
They are Hydrophilic-Aromatic
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Define Stereoisomer
Same formula, Different orientation
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Rectus vs Sinister are [BLANK] configuration
Absolute Stereoisomeric configuration
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Dextrorotatory vs Levorotatory are [BLANK] configuration
Optical rotation determined designated
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In determining the stereoisomerism of all amino acids except Cysteine L =? and that means
L = S = counter clockwise; the L config is only found in proteins or peptides
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In determining the stereoisomerism of all amino acids except Cysteine R =? and that means
- R = D = Clockwise;
- the D config is not found in proteins or Peptides
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In determining the stereoisomerism of Cysteine L =? and that means
L = R = Clockwise rotation; this config is found in proteins or peptides
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In determining the stereoisomerism of Cysteine D =? and that means
D = S = Counterclockwise; this config is not found in proteins or peptides
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Rule for determining the # of stereoisomers for amino acids
The G, I, T exception
- 17 aa's + 2aa's + 1 aa = 20aa
- 1cc + 2cc's (I, T) + 0cc (G)
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Formula for determining the # of Stereocenters
- # stereocenters = # chiral centers = n
- 2n
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ACRONYMS: GAV LIM FWP
Hydrophobic group of amino acids
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ACRONYMS: GAV LIMP
Aliphatic amino acids
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ACRONYMS: FW
Hydrophobic aromatic amino acids
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ACRONYMS: CDESTY HKR NQ
Hydrophilic amino acids
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ACRONYMS: CDESTY HKR
Amino acids with an ionizable side chain
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