Amino Acids

Question 1

Proline

Answer 1

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.

Question 2

What are the amino acids have side chains which are uncharged rings, linear or branched hydrocarbon chains, with an even distribution of charge?

Answer 2

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.

Question 3

Glycine

Answer 3

non-polar, R-group = H. This aa is the exception in that is the only aa that is achiral. (not chiral)

Question 4

Alanine

Answer 4

non-polar, R-group = methyl

Question 5

Isoleucine

Answer 5

non-polar, R-group = branched chain hydrocarbon

Question 6

Leucine

Answer 6

non-polar, R-group = branched chain hydrocarbon

Question 7

Valine

Answer 7

non-polar, R-group = branched chain hydrocarbon

Question 8

Methionine

Answer 8

non-polar, R-group contains Sulfur

Question 9

Phenylalanine

Answer 9

non-polar, R-group contains an aromatic ring

Question 10

Tryptophan

Answer 10

non-polar, R-group contains an aromatic ring

Question 11

What kind of interactions are there between amino acids with non-polar R-groups?

Answer 11

Non-polar side chains are hydrophobic and tend to aggregate in water to avoid the polar H2O, forming hydrophobic interactions.

Question 12

Hydrophobic effect

Answer 12

formation of the hydrophobic core in the inside of the proteins. It is a major force behind the folding of globular proteins

Question 13

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)

Answer 13

Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine

Question 14

Which amino acids have an aromatic ring associated with it’s R-group.

Answer 14

Tryptophan (non-polar), Phenylalanine (non-polar), Tyrosine (R-group = OH; polar, uncharged)

Question 15

Which amino acids have a hydroxyl (-OH) group associated with the R-group?

Answer 15

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.

Question 16

Cysteine

Answer 16

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.

Question 17

Post-translational modification

Answer 17

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.

Question 18

Disulfide bonds

Answer 18

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.

Question 19

cystiene

Answer 19

the resulting dimer of two cysteines covalently attached to one another via S-S disulfide bond.

Question 20

What are the amino acids with polar and uncharged R-groups?

Answer 20

Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine

Question 21

Serine

Answer 21

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.

Question 22

Threonine

Answer 22

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.

Question 23

Tyrosine

Answer 23

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.

Question 24

What amino acids have polar and charged side chains?

Answer 24

Acidic:
Glutamic acid (glutamate), aspartic acid (aspartate)
Basic:
Arginine (positive charg), lysine (positive charge) histidine (charge is between 0 and +1) (ie. HAL)

Question 25

Acidic amino acids

Answer 25

(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.

Question 26

Basic Amino Acids

Answer 26

(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)

Question 27

Which amino acids undergo hydrophobic reactions?

Answer 27

Non-polar

Question 28

Which amino acids undergo H-bonds?

Answer 28

Any polar amino acid

Question 29

Which amino acids undergo disulfide bonds?

Answer 29

cysteine

Question 30

Which amino acids undergo ionic bonds?

Answer 30

polar, charged amino acids can do both H-bond and ionic bonds

Question 31

Low pKa means _____ , low pH means _____

Answer 31

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