Lecture #04: Amino Acids Flashcards
What To Focus On When Studying Amino Acids
• What’s Important?
○ Amino acid’s ionizable groups-acid base properties.
○ Amino acid’s chemical & structural features.
○ Their classification-important for types of noncovalent interactions that determine protein structure.
Nonessential vs. Essential Amino Acids
• Two basic groups of amino acids. Nonessential (can be made in the body) and essential (must come from diet). Terms can be very misleading.
○ We make our nonessential amino acids from specific TCA cycle intermediates.
Amino Acids Chiral or Achiral?
• With four different groups connected to the tetrahedral alpha-carbon atom, alpha-amino acids are chiral (optically active): they may exist in one or the other of two mirror-image forms, called the L and D isomer.
○ Only L amino acids are constituents of proteins. The answer why is not known.
L Isomer vs. D Isomer
In L isomer, amino group is on the left. In D isomer, amino group is on the right.
Amino Acids at pH of 7
• All amino acids have at least two charged groups when they are free and in solution with a neutral pH of 7. They have an amino group which is protonated (NH3+) and a carboxyl group which is deprotonated (COO-).
Amino and Carboxyl Groups of Amino Acids at Different pHs
○ In an acid solution, the amino group is protonated (NH3+) and the carboxyl group is not dissociated (COOH). As the pH is raised, the carboxylic acid is the first group to give up a proton, because its pKa is near 2. The dipolar form persists until the pH approaches 9, when the protonated amino group loses a proton.
R Group Confers…
• The R group confers unique characteristics to each amino acid: vary in charge, shape, ability to H-bond, hydrophobicity, chemical reactivity.
Categories of Amino Acids
• Classifying amino acids ultimately depends on the R group. The scheme we’ll use to sort them is this.
○ Hydrophobic amino acids with nonpolar R groups. (Aliphatic - a chain, or aromatic - conjugated ring structure).
○ Polar amino acids with neutral R groups but the charge is not evenly distributed.
○ Positively charged amino acids with R groups that have a positive charge at physiological pH (7.4).
○ Negatively charged amino acids with R groups that have a negative charge at physiological pH.
Polar Charged Negative Amino Acids
• Polar charged, negative amino acids are asparate and glutamate. In some amino acids these side chains accept protons, which neutralize the negative charge, which can thus be a functionally important ability.
Asparate
Negatively charged.
Glutamate
Negatively charged.
Polar Charged Positive Amino Acids
• Polar charged, positive amino acids are lysine, arginine, and histidine. The positive charge render these highly hydrophilic.
Lysine
Positively charged. Lysine have long side chains that terminate with groups that are positively charged at neutral pH. Note that their R groups have dual properties-the carbon chains constitute a hydrocarbon backbone, similar to the amino acid leucine, but the chain is terminated with a positive charge.
Arginine
Positively charged. Arginine have long side chains that terminate with groups that are positively charged at neutral pH. Note that their R groups have dual properties-the carbon chains constitute a hydrocarbon backbone, similar to the amino acid leucine, but the chain is terminated with a positive charge.
Histidine
Positively charged. ○ Histidine contains an imidazole group, an aromatic ring that also can be positively charged. With a pKa value near 6, it makes this group unique in that it can be uncharged or positively charged near neutral pH. Often found on active site of enzymes, where the imidazole ring can bind and release protons in course of enzymatic reactions.
Polar Uncharged Amino Acids
• Polar uncharged amino acids are neutral overall, yet are polar because the R group contains an electronegative atom that hoards electrons. Has 3 divisions.
Serine, Threonine, Tyrosine, Cysterine, Asparagine, Glutamine.
Serine
○ Serine, threonine, and tyrosine contains OH groups. The electrons in the OH bond are attracted to the oxygen atom, making it partly negative, which in turn makes the H partially positive. The OH group makes them more hydrophilic and reactive than their respective nonpolar counterparts alanine, valine, and phenylalanine.
§ Serine can be thought of as a version of alanine with a OH group attached to the methyl group.
Threonine
Polar uncharged. Serine, threonine, and tyrosine contains OH groups. The electrons in the OH bond are attracted to the oxygen atom, making it partly negative, which in turn makes the H partially positive. The OH group makes them more hydrophilic and reactive than their respective nonpolar counterparts alanine, valine, and phenylalanine.
§ Threonine resembles valine with a hydroxyl group in place of one of the valine methyl groups.
Tyrosine
Polar uncharged. Serine, threonine, and tyrosine contains OH groups. The electrons in the OH bond are attracted to the oxygen atom, making it partly negative, which in turn makes the H partially positive. The OH group makes them more hydrophilic and reactive than their respective nonpolar counterparts alanine, valine, and phenylalanine.
§ Tyrosine is similar to phenylalanine but has a hydrophilic hydroxyl group attached to the large aromatic ring.
Tyrosine is amphipathic. Both hydrophilic and lipophilic.
Cysteine
Polar uncharged. Cysterine is structurally similar to serine but contains a sulfhydryl or thiol (SH) group in place of OH. It’s much more reactive and can completely lose a proton at slightly basic pH to form the reactive thiolate group.
Asparagine
Polar uncharged. Asparagine and Glutamine contain a terminal carboxamide.
Glutamine
Polar uncharged. Asparagine and Glutamine contain a terminal carboxamide.
Nonpolar Aliphatic Amino Aids
The amino acids having side chains consisting only of hydrogen and carbon are hydrophobic. Glycine, alanine, valine, leuine, isoleucine, methionine, proline.
Glycine
Nonpolar aliphatic. Glycine’s side chain is H, so it is achiral.
Alanine
Nonpolar aliphatic.
Valine
§ Aliphatic nonpolar amino acids with branched chains are valine, leuine, and isoleucine.
Leucine
§ Aliphatic nonpolar amino acids with branched chains are valine, leuine, and isoleucine.
Isoleucine
§ Aliphatic nonpolar amino acids with branched chains are valine, leuine, and isoleucine.
Methionine
Methionine contains a largely aliphatic side chain that includes a thioether (S) group. Nonpolar aliphatic.
Proline
Nonpolar aliphatic. Proline differs in that its side chain is bonded to both the alpha carbon and the nitrogen atom. Its structure makes it more conformationally restricted.
Nonpolar Aromatic
Aromatic ring structure permits absorption of UV light.
Phenylalanine, tryptophan, and tryrosine.
Phenylalanine
Nonpolar aromatic. Aromatic ring structure permits absorption of UV light.
Tryptophan
Nonpolar aromatic. Aromatic ring structure permits absorption of UV light.
Noncovalent Role
• Noncovalent interactions contribute to protein folding and reactivity.
pH and pKa Relationship
• At pH < pKa, H+ on, protonated. At pH > pKa, H+ off, deprotonated.
Hydrogen
• H is common to all amino acids, but remember it is NOT a functional group.
