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Amino Acids II
Give the category
| Question | Answer |
|---|---|
| Glycine | Hydrophobic |
| Alanine | Hydrophobic |
| Proline | Hydrophobic |
| Valine | Hydrophobic |
| Leucine | Hydrophobic |
| Isoleucine | Hydrophobic |
| Methionine | Hydrophobic |
| Tryptophan | Hydrophobic |
| Phenylalanine | Hydrophobic |
| Serine | Polar (uncharged) |
| Threonine | Polar (uncharged) |
| Tyrosine | Polar (uncharged) |
| Asparagine | Polar (uncharged) |
| Glutamine | Polar (uncharged) |
| Cysteine | Polar (uncharged) |
| Lysine | Positively charged |
| Arginine | Positively charged |
| Histidine | Positively charged |
| Aspartate | Negatively charged |
| Glutamate | Negatively charged |
| Name the two amino acids that are acidic, but lose their protons at physiological pH | Glutamate (glutamic acid) and Aspartate (aspartic acid) |
| Name the seven amino acids that can be readily ionized | cysteine, tyrosine, lysine, arginine, histidine, aspartic acid, glutamic acid |
| What are the pKa values for amino acids with terminal carboxyl or amino groups? | carboxyl = 3.1, amino = 8.0 |
| What are the four amino acids whose three-letter abbreviations do not match the first three letters of their names, and what are the abbreviations? | asparagine (Asn), glutamine (Gln), isoleucine (Ile), and tryptophan (Trp) |
| What are the four amino acids that have variable abbreviations, and what are the abbreviations (give both three-letter and single letter)? | asparagine OR aspartic acid can be denoted by Asx and by B ; glutamine OR glutamic acid can be denoted by Glx and by Z |
| Which end of a polypeptide chain is considered to be the beginning? | The amino end (N-terminal) |
| What are the single letter abbreviations for glutamine and glutamic acid (glutamate)? | Q and E, respectively |
| What are the two isomer types of an amino acid? Which one forms peptide bonds with other amino acids to form protein? | D and L ; L |
| What are the torsion angles (phi and psi) of the single bonds adjacent to a peptide bond? | phi = -80 deg ; psi = +85 deg |
| What is the word used to describe the side chains of amino acids that are non-aromatic and that have unbroken hydrocarbon chains? | aliphatic |
| Name the four amino acids with aromatic side chains | phenylalanine, tyrosine, tryptophan, histidine |
| What are the three amino acids containing hydroxyl groups in their side chains? Which two are aliphatic? | serine, threonine, and tyrosine ; serine and threonine |
| Which two polar amino acids have side chains containing carboxamide functional groups? | asparagine and glutamine |
| Which amino acid is very reactive in terms of the formation of disulfide bonds? What is the name of the structure formed when two of these amino acids form a bond between their side chains (a disulfide bond)? | cysteine ; cystine |
| What is the name of the functional group found in the side chains of negatively charge amino acids? | carboxylate |
| Almost all peptide bonds form what type of stereoisomer? | trans |
| Which amino acid is typically involved in a cis stereoisomer of a peptide bond between to adjacent amino acids? | proline |
| Name the three amino acids that have branched beta-carbons (two carbons bound to the beta carbon as opposed to only one carbon-carbon bond). What does the branching prevent in terms of participation in polypeptides. | valine, isoleucine, threonine ; alpha-helices tend to destabilize due to steric "clashing" between the side chains and the backbone |
| Name three amino acids that destabilize alpha-helices due to the proximity of their H-bond donating or accepting side chains to the backbone. | serine, asparagine, aspartate |
| Which amino acid has a ring structure that binds directly to the alpha-carbon and to the N-terminus? What are the consequences of this stucture in terms of participation in polypeptide chains? | proline ; the ring prevents proline from participating in alpha-helices, due to the fit requirement of a helix (doesn't fit). |
| After a peptide bond forms between two amino acids, what happens to the carboxyl and amino functional groups as a result of the bond? What by-product is produced as a result of this bond? | The carboxyl group becomes a carbonyl group, and the amino group changes from a primary amine to a secondary amine. A water molecule is given off as a by-product |
| Are most alpha-helices found in proteins right or left-handed? Why is this? | Right handed ; This is due to the energetically favorable right handed conformation vs. the left-handed conformation, which has a greater degree of steric hindrance among the units of the peptide backbone. |
| When an alpha-helix is formed, it is between the carbonyl and amino groups of the peptide backbone, spaced how many residues apart? | 4 |
| Which amino acid has no chiral carbons? | glycine |
| Name the four amino acids with aliphatic side chains | valine, leucine, isoleucine, methionine |
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