Amino Acids: Properties, Structure, and Function, Exams of Biochemistry

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Glycine, Gly, G non-polar, aliphatic Alanine, Ala, A non-polar, aliphatic Valine, Val, V non-polar, aliphatic Leucine, Leu, L non-polar, aliphatic Isoleucine, Ile, I non-polar, aliphatic

Methionine, Met, M Nonpolar, aliphatic R Groups Proline, Pro, P Nonpolar, aliphatic Phenylalanine, Phe, F Non-polar aliphatic aromatic Tryptophan, Trp, W Non-polar, aromatic R groups Serine, Ser, S Polar, neutral, hydrophilic

Lysine, Lys, K Polar basic, positive charge Arginine, Arg, R Polar basic, positive charge Histidine, His, H Polar basic, positive charge Imidazole side chain of histidine aromatic ring with two nitrogens pka of side chain is 6 - so at a physiological pH the side chain is neutral amide then will be protonated at a higher pH Aspartate, Asp, D Polar acidic, negative charge

Glutamate, Glu, E Polar acidic, negative charge essential amino acids Amino acids that are needed, but cannot be made by the body; they must be consumed by diet essential amino acids histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine nonessential amino acids amino acids that can be manufactured by the body in sufficient quantities and therefore do not need to be consumed regularly in our diet nonessential amino acids alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, tyrosine Histidine ionization

• Histidine can bind or release protons near physiological pH
• With pKa near 6 the imidazole group can be uncharged or positively charged
• Often found at active sites of enzymes

pKa = 10. NH3+ (acid) --> NH2 (base) Arginine pKa pKa = 12. Peptide Structure

• central carbon
• amine group
• carboxyl group
• hydrogen atom
• R group Peptide bonding covalent bonding between two amino acids
• condensation reaction
• water molecule by-product Hydrolysis break down of peptide bond
• addition of water to separate amino acids Hydrophobic effect the observed tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules Polar amino acid side chains electron hoarding, but neutral charge
• due to OH and SH functional groups positively charged amino acids hydrophilic basic side chain

• at physiological pH negatively charged amino acids

hydrophilic acidic side chain

• at physiological pH How many amino acids are there? 20 L isomer
• OH or - NH2 on the left of the chiral carbon (sugars)
• most common form for amino acids
• counterclockwise D isomer
• OH or - NH2 on right of the chiral carbon (sugars)
• clockwise Zwitterionic form amino acid that exists at physiological pH i.e. with the amino group protonated and the carboxyl group ionized and both groups covalently attached to the alpha carbon yielding a dipolar ion. In acidic solutions... both groups are protonated on amino acid In basic solutions... both groups are deprotonated on amino acid cooperative behavior Allows rapid binding of oxygen in the lungs and easy release at the tissues where oxygen is required Sequential Mechanism of Cooperative Binding stepwise increase in oxygen affinity. The more oxygens that are bound to the hemoglobin the more affinity it has for other oxygens. Concerted Mechanism of Cooperative Binding