Module 3: Protein structure/function

Question 1

Primary structure

Answer 1

sequence of aa in polypeptide chain

linear, aa joined by peptide bonds

Question 2

Secondary structure

Answer 2

driven primarily by peptide backbone interactions
stabilized by H bonds
alpha helix/beta sheet

Question 3

Tertiary structure

Answer 3

driven primarily by side-chain interactions

fold w hydrophobic side chains sheltered inside

Question 4

Quaternary structure

Answer 4

2 or more chains combine

Question 5

Amino acid structure

Answer 5

COO-
                  |
H3N+\_\_ Calpha \_\_H
                  |
                 R (side chain)

Question 6

Chirality

Answer 6

any molecules whose reflection in a mirror cannot be superimposed
attached: 4 non-identical groups

Question 7

L-chirality

Answer 7

L-aa rotates polarized light to the left

***only glycine achiral

Question 8

Peptide bond

Answer 8

formed by a nucleophilic addition-elimination reaction between the carboxyl and amino groups of adjacent amino acids
rigid, planar bond due to resonance delocalization of e-
not a lot of rotation

Question 9

N-terminal

Answer 9

beginning

amino group

Question 10

C-terminal

Answer 10

end

carboxyl group

Question 11

Non-polar, aliphatic aa

Answer 11

Gly (G), Ala (A), Pro (P), Val (V), Leu (L), Ile (I), Met (M)

• non polar and hydrophobic
• Ala, Val, Leu: cluster within pr-, stabilize pr- structures
• Gly, Ala: ambivalent (can reside anywhere on pr-)
• Pro: R forms covalent bond w a-amino group, found on pr- surface
• Met: sulfur containing R group

Question 12

Polar, uncharged R groups

Answer 12

Ser (S), Thr (T), Cys (C), Asn (N), Gln (Q)
- can form HBs w water/ other polar mol
- Ser, Thr: found on pr- surface
OH of serine great nucleophile
- Cys: polar side chain form HBs w water, found on pr- surface, SH group great nucleophile
- Asn, Gln: amide counterparts to Asp/Glu, have nonionizable uncharged polar side chains

Question 13

Aromatic R groups

Answer 13

Phe (F), Tyr (Y), Trp (W)

• hydrophobic, can absorb UV light at 280nm
• Phe; most hydrophobic aa
• Tyr: ionizable group, can form HBs
• Trp: bulky aa

Question 14

Negatively charged R groups

Answer 14

Asp (D), Glu (E)

• carry neg charge at pH 7
• hydrophilic, typically found on pr- surface

Question 15

Positively charged R groups

Answer 15

Lys (K), Arg (R), His (H)

• basic side chain character, very polar, found on pr- exterior/ substrate binding clefts
• His: least basic, imidazole ring

Question 16

Multisubunit proteins

Oligomeric vs protomers

Answer 16

2/more polypeptides associated noncovalently
Oligomeric: if at least 2 are identical
Protomers: identical units

Question 17

Simple protein

Answer 17

contains only aa resides and no other chemical constituents

Question 18

Conjugate protein

prosthetic group

Answer 18

contain permanently associated chemical components in addition to aa
Prosthetic group: non-amino acid part