Amino Acids Flashcards
Learning the structure and classification of amino acids.
Proline
Non-Polar. Proline is the exception in which all other amino acids are α-amino acids. Proline is a secondary amine, therefore it is called an imino acid.
What are the amino acids have side chains which are uncharged rings, linear or branched hydrocarbon chains, with an even distribution of charge?
i.e. non-polar (hydrophobic/lypophillic) R- goups.
Glycine, Alanine, Isoleucine, Leucine, Valine, Methionine, Phenylalanine, Tryptophan, Proline.
Exceptions: Met and Trp have a polar atom, but the electronegativity is masked by surrounding hydrocarbons.
Glycine
non-polar, R-group = H. This aa is the exception in that is the only aa that is achiral. (not chiral)
Alanine
non-polar, R-group = methyl
Isoleucine
non-polar, R-group = branched chain hydrocarbon
Leucine
non-polar, R-group = branched chain hydrocarbon
Valine
non-polar, R-group = branched chain hydrocarbon
Methionine
non-polar, R-group contains Sulfur
Phenylalanine
non-polar, R-group contains an aromatic ring
Tryptophan
non-polar, R-group contains an aromatic ring
What kind of interactions are there between amino acids with non-polar R-groups?
Non-polar side chains are hydrophobic and tend to aggregate in water to avoid the polar H2O, forming hydrophobic interactions.
Hydrophobic effect
formation of the hydrophobic core in the inside of the proteins. It is a major force behind the folding of globular proteins
What are the amino acids with uncharged, polar R-groups? (one or more electronegative atoms (O, N, S) in the side chain, and electrically neutral at physiological pH)
Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine
Which amino acids have an aromatic ring associated with it’s R-group.
Tryptophan (non-polar), Phenylalanine (non-polar), Tyrosine (R-group = OH; polar, uncharged)
Which amino acids have a hydroxyl (-OH) group associated with the R-group?
Serine, Threonine and Tyrosine. These are polar and uncharged at physiological pH. These can undergo H-bonding interactions with other molecules. These amino acids are sites for post-translational modification, in which phosphates or carbs attach to their -OH group.
Cysteine
Polar, uncharged R-group. Contains a sulfhydryl (-SH) group. Undergoes H-Bonding interactions, but cysteine is the only amino acid that can form disulfide bonds. Cysteine is modified into selenocysteine, in which selenium replaces the S of cysteine.
Post-translational modification
Amino acids provide sites for post-translational modifications, which are essential in some proteins.
1) attachment of phosphates or carbs to the -OH group of serine, threonine or tyrosine.
2) Proline and Lysine are hydroxylated in mature collagen.
Disulfide bonds
Strong bonds formed upon an oxidation reaction between two cysteines. Cysteine is the only amino acid that can form S-S bonds. The resulting dimer of cysteines is named cystine. As opposed to H-bonds and ionic bonds, which are weak bonds, disulfide bridges are covalent, strong bonds.
cystiene
the resulting dimer of two cysteines covalently attached to one another via S-S disulfide bond.
What are the amino acids with polar and uncharged R-groups?
Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine
Serine
polar, uncharged hydroxyl (-OH) R-group. Can undergo H-bond interactions. Also, can be post-translationally modified by attaching a phosphate or carb to the -OH group.
Threonine
polar, uncharged hydroxyl (-OH) R-group. Can undergo H-bond interactions. Also, can be post-translationally modified by attaching a phosphate or carb to the -OH group.
Tyrosine
polar, uncharged hydroxyl (-OH) R-group. Can undergo H-bond interactions. Also, can be post-translationally modified by attaching a phosphate or carb to the -OH group. This amino acid also contains and aromatic ring.
What amino acids have polar and charged side chains?
Acidic:
Glutamic acid (glutamate), aspartic acid (aspartate)
Basic:
Arginine (positive charg), lysine (positive charge) histidine (charge is between 0 and +1) (ie. HAL)
Acidic amino acids
(GLAS [GLutamate and Aspartate) Polar and charged; Glutamic acid (a.k.a. glutamate) and aspartic acid (a.k.a. aspartate). These have side chains contain -COOH groups that are dissociated and negatively charged at physiological pH.
Basic Amino Acids
(HAL) Side chain positively charged at physiological pH, except His.
Arginine (positive charg), lysine (positive charge) histidine (charge is between 0 and +1) (ie. HAL)
Which amino acids undergo hydrophobic reactions?
Non-polar
Which amino acids undergo H-bonds?
Any polar amino acid
Which amino acids undergo disulfide bonds?
cysteine
Which amino acids undergo ionic bonds?
polar, charged amino acids can do both H-bond and ionic bonds
Low pKa means _____ , low pH means _____
Low pKa means a stronger acid (more easily let’s go of its H+. Low pH solution means that it is an acidic solution. pKa (1) sauce. pKa near 1 is really strong and pH at 1 is extremely acidic
