Amino Acids - general

Question 1

Amino acid

Answer 1

building block of proteins; carboxyl group + amino group both attached to a carbon with a R aka side-chain group

Question 2

Protein

Answer 2

linear polymers of amino
acids connected by peptide bonds

Question 3

Steroisomerism in a-amino acids

Answer 3

• All amino acids are chiral except for glycine
• Natural proteins contain L amino acids (only a few cases with D-type)
• A very small number of short peptides and peptide antibiotics contain D-
  amino acids

Question 4

R-S system

Answer 4

• The higher the atomic number of the immediate substituent atom, the higher the
  priority.
  e.g. O > N > C > H
• If two substituents have the same immediate substituent atom,
  evaluate atoms progressively further away from the chiral center until a difference
  is found.
  e.g. -C-O > -C-C > -C-H

Question 5

Hydrophobic

Answer 5

avoids aqueous environment; molecules are non-polar and uncharged

these amino acids are usually buried in the hydrophobic core of this protein

Question 6

Aliphatic

Answer 6

carbon atoms are joined together in straight or branched open chains rather than in rings

Question 7

aromatic

Answer 7

contains an aromatic ring system

Question 8

hydrophilic

Answer 8

interacts with water; molecules are polar and charged

these amino acids are usually found on the protein surface of the protein

Question 9

What amino acids sidechains have torsion angles?

Answer 9

ALL except Alanine (Ala) and Glycine (Gly)

Question 10

gauche vs anti-gauche

Answer 10

both are staggered conformations that are 60 degree apart

anti is more stable with lower-energy conformation

Question 11

different side-chain conformations do NOT have . . .

Answer 11

equal distribution over the dihedral angle space

Question 12

rotamer

Answer 12

aka rotational isomer

low energy side-chain conformations

Question 13

How are rotamers knowledge-based?

Answer 13

Rotamers are based on statistical analysis of sidechain conformations . . .

. . . in known protein structures through clustering observed conformations . . .

. . . or dividing torsion angle space into bins and determining an average conformation in each bin

Question 14

Rotamer library

Answer 14

collection of rotamers for each residue type

contains info about conformations and frequency of each conformation

different types of libraries based on categories (such as backbone dependent or independent)

Question 15

PI

Answer 15

iso electric point where net charge is 0

Question 16

at acidic ph, carboxyl group is protonated and amino acid is . . .

Answer 16

in the cationic form

Question 17

t neutral pH, the carboxyl group
is deprotonated but the amino
group . . .

Answer 17

is protonated

net charge is 0 and ion are called Zwitterions

Question 18

At alkaline pH, the amino group is
neutral –NH 2 and the amino acid
is . . .

Answer 18

in the anionic form.

Question 19

anionic form

Answer 19

molecule or group that has gained one or more electrons, resulting in a negative charge

Question 20

cationic form

Answer 20

molecule or group that has lost one or more electrons, resulting in a positive charge

Question 21

protonate

Answer 21

molecules adds a proton (H+); gaining a positive charge

Question 22

The model pKa for a particular
amino acid residue is determined for
the case when the titratable group is . . .

Answer 22

completely accessible to the solvent
and minimally perturbed by the
surrounding environment.

Question 23

a-carboxy group is much more acidic than . . .

Answer 23

that in carboxylic acids

Question 24

amino group is slightly less basic than . . .

Answer 24

in amines (or more acidic)

Question 25

amino vs amine

Question 26

for sigma and pi bonds: the initial bond is ? and every bond after is ?

Answer 26

sigma, pi

Question 27

atom naming in PDB

Answer 27

format = 123 1 - atomic symbol (C, N, O, S) 2 - remoteness indicator (Greek letters) 3 - branch designator (1, 2, 3, . . .)