Section 2

Question 1

Name the 20 amino acids

Answer 1

Look at chart online

Question 2

What are the five groups that side chains can be assorted into according to their polarity and charge?

Answer 2

Nonpolar: Aliphatic or Aromatic

Polar: Uncharged, Negatively charged, Positively charged

Question 3

What are the non-polar, aliphatic amino acids?

Answer 3

Glycine (Gly, G)
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine (Ile, I)
Methionine (Met, M)
Proline (Pro, P)

Question 4

What are the non-polar, aromatic amino acids?

Answer 4

Phenylalanine (Phe, F)
Tyrosine (Tyr, Y)
Tryptophan (Trp, W)

Question 5

What are the polar, uncharged amino acids?

Answer 5

Cysteine (Cys, C)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Serine (Ser, S)
Threonine (Thr, T)

Question 6

What are the polar, negatively charged amino acids?

Answer 6

Aspartate (Asp, D)
Glutamate (Glu, E)

Question 7

What are the polar, positively charged amino acids?

Answer 7

Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)

Question 8

What does nonpolar, aliphatic side chain mean for an amino acid?

Answer 8

• composed of hydrocarbon chains (–CH2—) which are nonpolar and quite hydrophobic
• this causes these AAs to interact with other hydrophobic AAs, usually in the interior of proteins, to minimize their contact with water
• this is a major driving force behind PROTEIN FOLDING

Question 9

Which amino acid has the smallest side chain out of the 20 amino acids?

Answer 9

Glycine (only a single H atom as its side chain)

Question 10

________ is nonpolar, but since it has only a single H atom as its side chain, it contributes little to hydrophobic effects.

Answer 10

Glycine

Question 11

In which amino acid does the side chain connect to its own amino acid? What does this result in?

Answer 11

Proline. The resulting 5-membered ring causes proline to be very rigid and thus limits its possible conformations.

Question 12

Which one out of the nonpolar, aromatic amino acids is the most hydrophobic, and why?

a) F
b) Y
c) W

Answer 12

a) F (phenylalanine)

The tyrosine (Y) hydroxyl group and the tryptophan (W) nitrogen can form hydrogen bonds, and thus impart some polarity to these residues.

Note: All of them can participate in hydrophobic interactions

Question 13

How can we tell the concentration of Phe, Tyr, and Trp in a protein?

Answer 13

Since the aromatic rings absorb ultraviolet light.

Note: tryptophan and tyrosine are able to absorb much more UV light than phenylalanine

Question 14

_______, _________ side chains can interact extensively with water, or with atoms in other side chains, through hydrogen bonds.

Answer 14

Polar, uncharged

Question 15

What is special about cysteine?

Answer 15

• contains a sulfhydryl group
• two cysteines that are in close proximity to each other can be oxidized to form a disulfide bond (a covalent bond between the two sulfhydryl groups)
• this bond can enhance protein stability
• cysteine residues are also important for the catalytic functions of many enzymes, as the deprotonated -SH is a good nucleophile (e- pair donor)

Question 16

What are features of Asn and Gln side chains?

Answer 16

They contain an amide group that can act as a donor or acceptor of electrons.

They also contain a carbonyl group (C=O) that can participate in hydrogen bonding and dipole-dipole interactions.

Question 17

What is the amide group important for in N and Q side chains?

Answer 17

It can act as a donor or acceptor of electrons

Question 18

What is the carbonyl group, and what is it important for in N and Q?

Answer 18

it is C=O

It can participate in hydrogen bonding and dipole-dipole interactions

Question 19

What are features of S and T side chains?

Answer 19

they have hydroxyl (OH) group on the side chain, which is capable of forming hydrogen bonds.

these can also be phosphorylated (along with the OH of Tyrosine) by kinases, resulting in protein modifications.

Question 20

What can happen to the OH group on serine/threonine/tyrosine side chains? What does this result in
?

Answer 20

The OH can be phosphorylated, which results in protein modifications

Question 21

What are features of D and E side chains?

Answer 21

• contain a carboxyl group and therefore carry a negative charge at pH 7.0 (i.e. they are acidic)

Question 22

True or false:

Aspartate and glutamate can be referred to as aspartic acid and glutamic acid.

Answer 22

True

Question 23

The amino acids that carry a positive charge at pH 7.0 are called ______, ________ and they include ______, _______, _______

Answer 23

The amino acids that carry a positive charge at pH 7.0 are called polar, positively charged and they include lysine, arginine, histidine.

Question 24

What does it mean when amino acids carry a pos/neg charge at pH 7.0?

Answer 24

If they carry a positive charge at pH 7.0 they are basic, if they carry a negative charge they are acidic

Question 25

Match the side chain group (amino, guanidinium, or imidazole) with each of the following:

• Arginine
• Lysine
• Histidine

Answer 25

• Lysine: amino group
• Arginine: guanidinium group
• Histidine: Imidazole group

Question 26

Where are charged amino acids usually located (on exterior or interior of protein) and why?

Answer 26

Charged amino acids are usually very hydrophilic and typically make ionic and hydrogen bonding interactions with H2O. Therefore they tend to be on the exterior of proteins, in contact with water.

Question 27

These side chains are very hydrophilic, so they tend to be located in the active site of many enzymes, such as DNA polymerase:

Answer 27

Charged amino acid side chains

Question 28

When an amino acid sequence is given, is it written and read from:

a) The C-terminus to the N-terminus, left to right
b) The N-terminus to the C-terminus, left to right

Answer 28

b) The N-terminus to the C-terminus, left to right

Question 29

What is a buffer?

Answer 29

A solution with a pH that does not change very much when H3O+ or OH- ions are added.

It contains approximately equal amounts of a weak acid and its conjugate base

Question 30

What does most of the energy required to unfold proteins go towards?

Answer 30

It goes mainly towards disrupting the stabilizing hydrophobic effect

Question 31

What is an imino group?

Answer 31

C=N