CW2: Amino acid structure

Question 1

Why is rotation around a peptide bond not possible?

Answer 1

The peptide bond is planar due to its partial double-bond character, which limits the rotation angle between amino acids

Question 2

What is the amino acid with the simplest side chain?

Answer 2

Glycine

Question 3

What is the name and structure of the intermediate between the two forms of a peptide? Why is it unable to rotate?

Answer 3

Resonance hybrid

It cannot rotate due to the partial double bonds making it a planar molecule

Question 4

Name the amino acids with polar, positively charged side chains and give their three- and one-letter abbreviations

Answer 4

Lysine / Lys / K

Arginine / Arg / R

Histidine / His / H

Question 5

Between which bonds in a peptide is free rotation permitted? What is the name of the angles of these bonds, and why are certain values of these angles not permitted?

Answer 5

Free rotation is permitted between:

• C_α –C bond: psi (Ψ) angle
• N–C_α bond: phi (Φ) angle

Certian values aren’t permitted because of steric hindrance (side chains hitting each other).

Question 6

How can serine and threonine be modified after synthesis? Explain this process if there were a lack of O₂ in the cell.

Answer 6

Phosphorylation: adding PO₃^2– to the amino acid

Receptor discovers lack of O₂ → Cell nucleus responds with a phosphorylation reaction → Can turn off signal as well using phosphatase (i.e. it is a reversible reaction)

Question 7

Why are localised pH effects very influential on histidine?

Answer 7

Its pK is 6.5 which is close to a pH of 7, therefore histidine can either accept or donate protins. This means that a small change in pH in either direction can cause a large change in the properties of amino acid chains containing histidine

Question 8

What are the special properties of proline?

Answer 8

• Not very polar and not very non-polar
• Side chain is chemically linked to the backbone so not very flexible

Question 9

Name the amino acids with polar, uncharged side chains and give their three- and one-letter abbreviations

Answer 9

Serine / Ser / S

Threonine / Thr / T

Asparagine / Asn / N

Glutamine / Gln / Q

Cysteine / Cys / C

Question 10

What is the bond between two amino acids? How does it form?

Answer 10

Peptide bond

Question 11

W

Question 12

Which amino acids have hydroxyl groups and what influence does this have on their behaviour?

Answer 12

• Tyrosine
• Serine
• Threonine

They can be modified after synthesis (e.g. phosphorylated)

Question 13

Why do we often say ‘aspartate/glutamate’ not ‘aspartic acid/glutamic acid’?

Answer 13

These amino acids tend to exist negatively charged (because their pKs are approx. 4.4 at pH 7, so they are less protonated (i.e. pH is higher than pK) so protons are given up), hence ‘–ate’

Question 14

Name the amino acids with non-polar, aromatic side chains and give their three- and one-letter abbreviations

Answer 14

Phenylalanine / Phe / F

Tryptophan / Trp / W

Tyrosine / Tyr / Y

Question 15

Which amino acids have sulfur in their side chains? What are the differences in their properties?

Answer 15

Methionine and cysteine

The sulfur in methionine is buried in the side chain so has no large bearing on its properties

Cysteine can form dislfide bonds with other amino acids becuase its sulfur is at the end of the side chain

Question 16

At pH 7, which amino acids have negatively charged side chains? What are their ‘acidic names’?

Answer 16

Aspartate (aspartic acid)

Glutamate (glutamic acid)

Question 17

Define ‘α-carbon’

Answer 17

The carbon to which the side chain is bonded

Question 18

What properties would you expect from a non-polar amino acid?

Answer 18

• Hydrophobicity
• Chiral (true of all amino acids except glycine
• Optical isomers (except glycine)
• Folding in aqueous solution to ‘trap’ the hydrophobic regions

Question 19

Name the amino acids with non-polar, aliphatic side chains and give their three- and one-letter abbreviations

Answer 19

Glycine / Gly / G

Alanine / Ala / A

Valine / Val / V

Leucine / Leu / L

Isoleucine / Ile / I

Proline / Pro / P

Methionine / Met / M

Question 20

What does the term ‘isoelectric point’ mean?

Answer 20

The pH at which an amino acid will not migrate in an electric field, i.e. the pH where the amino acid is neutral and in its zwitterion form

Question 21

Why are the variable/side/R groups of amino acids found on alternate sides of a polypeptide backbone?

Answer 21

They are usually bulky groups

Question 22

Why is a peptide bond planar?

Answer 22

Because it has partial double-bond character which limits the rotation between two amino acids

Question 23

Name the amino acids with polar, negatively charged side chains and give their three- and one-letter abbreviations

Answer 23

Aspartic Acid / Asp / D

Glutamic Acid / Glu / E

Question 24

Which amino acid is actually an imino acid? Why?

Answer 24

Proline because it has a secondary amine group (connected to two carbons)

Question 25

Which amino acids have positively charged side chains at pH 7?

Answer 25

• Lysine
• Arginine
• Histidine

Question 26

What disease does 4-hydroxyproline protect against that proline does not? What’s the structural difference between the two?

Answer 26

Scurvy

4-hydroxyproline is proline with a hydroxyl group on the fourth carbon