Amino Acids & Proteins: Primary Structure

Question 1

What are the four different levels of protein structure?

Answer 1

primary–AA sequence
secondary–ways they fold
tertiary–complete 3D structure
quaternary– spatial arrangement of polypeptides in a multi subunit protein

Question 2

Common features of amino acids: (6)

Answer 2

1. all proteins are linear polymers of alpha amino acids
2. amino and carboxyl grps are ionized at physiological pH
3. each of the 20 common have a different R group
4. alpha carbon is chiral: usually in the L configuration in proteins
5. either polar or non-polar
6. some have special chemical properties

Question 3

Which amino acids are considered hydrophobic?

Answer 3

ala, val, leu, ile, met, trp, pro, phe

Question 4

Facts about hydrophobic AAs (Ala, val, leu, ile): (3)

Answer 4

they have aliphatic side chains

the diversity of the side chain contributes to optimal packing in the protein interior

Question 5

Which AA is often chosen as replacement to determine amino acid function using site directed mutagenesis?

Answer 5

Ala

Question 6

Whats special about Met?

Answer 6

contains sulfur which can be oxidized to s double bond o or SO2 which can effect protein function
other than that it is relatively inert

Question 7

Trp?

Answer 7

largest amino acid

absorbs UV light most at 280 nm and can therefore be used to determine [protein]

Question 8

Phe?

Answer 8

dullllllllll

Question 9

Pro?

Answer 9

the only imino acid

the side chain connected to NH group causes kink in polypeptide chain

Question 10

What are the polar AAs?

Answer 10

gly, asn, gln, his, ser, thr, tyr, cys

Question 11

Gly?

Answer 11

simplest AA, side chain = H

Question 12

Asn & Gln?

Answer 12

uncharged amides of the acidic AAs asp and glu

can be H bond donors or acceptors

Question 13

His?

Answer 13

imidazole side chain which can be positively charged at neutral pH
can be buffer

Question 14

Ser, Thr, & Tyr?

Answer 14

all have hydroxy group
often nucleophiles in reactions and are proton donors or acceptors
OH can be covalently attached to other groups

Question 15

Tyr?

Answer 15

derivative of Phe and both are precursors of amino acid neurotransmitters

Question 16

Cys?

Answer 16

forms disulfide bonds with other cys’!! (sulfhydryl group)
provides covalent crosslinking
inside the cell (reducing) SH form outside the cell oxidized S-S form

Question 17

Charged amino acids?

Answer 17

asp, glu, lys, arg

Question 18

Asp & Glu?

Answer 18

negatively charged carboxyl side chains at pH 7

= acidic

Question 19

Lys & Arg?

Answer 19

positively charged side chains at pH 7

=basic

Question 20

What configuration are most AA in protein?

Answer 20

L (other config = D, enantiomer)

Question 21

If multiple chiral centres are present what system is used for configuration? what configuration are most amino acids?

Answer 21

R & S system, S

Question 22

what is pI?

Answer 22

the isoelectric point on a titration curve, which is a pH value at which the net charge of the molecule is 0
molecules with a lot of acidic AAs will have a low pI and vice versa

Question 23

What is a peptide bond?

Answer 23

an amide covalent linkage formed through dehydration of alpha carboxyl group

Question 24

What results when a peptide bond is formed? (7)

Answer 24

an H2O molecule is lost, no charge when bond is formed, very stable, rigid and planar, trans, uncharged but polar, partial double bond character

Question 25

How many bonds does each amino acid residue contribute along the polypeptide backbone?

Answer 25

3: N-Calpha, Ca-C, and C-N

Question 26

what constrains the rotation about the two other bonds?

Answer 26

steric hindrance